your book in progress was well worth the time reading. Thank you for sharing it. It contains many valuable concepts upon which can be built.

The book is also a nearly pure systems engineering (SE) text book. Of course you are right that SE is a valuable method to tackle some (but by far not all) of the complexity of a Seed Factory. And as you write in your book SE does not do the actual job. It "only" breaks down the enormous undertaking into more manageable tasks, allocates goals for each task such that their results will fit together to perform as the intended system. But of course it leaves each of the actual tasks like technical concepts, design, engineering analysis and detail design to be done; as your book says probably several times over for comparing design options and accommodating system changes. This is the bulk of the work into which most of the ingenuity and effort will have to go.

Your book gave me a better and deeper understanding of creating a Seed Factory. But as of now it still left me unsatisfied about some important points (I am aware that the book is work still in progress):

Automation and Efficiency
In several places your book claims that the Mature Factory (85% self reproducing) is expected to be more efficient than a traditional industry producing the same products. Your main argument is the high level of automation and hence low level of human labour. Your Mature Factory will be able to reproduce itself every few years (was it 7?). What will the Mature Factory to be reproduced consist of?  A few multi-purpose vehicles (maybe 50?), a few dozen agricultural machines, the workshop with all the machines for reproduction, a few hundred houses or apartments, community utilities. The highest number of repetition of the same item is probably housing and house hold equipment. Most of the machines and plants have either low or single repetition numbers for every reproduction cycle.
To automate this kind of low volume production means heavy investment in design work and complex automation machinery just to produce one copy every 7? years. And don't forget that also the maintenance, repair, disassembly and recycling is intended to be automated too and therefore the automation equipment needs to be reproduced too. And this should really be more efficient than the present industry producing thousands or more copies every year? -*1)- And even they use automation to a much lower level than 85%. Only car industry producing millions of cars per year use a high level of automation (but of course without reproduction of itself).
In my opinion this high level of automation is not needed on Earth in moderate climate zones. (This might be a remainder from lunar projects). People need a task for their health. With the intended level of automation the villagers would need to work just 1 hour per day. What will they do the rest of the day? Experience shows that people without a fulfilling task get lazy, unhappy, aggressive, unhealthy and die earlier. Working to build, maintain and supply the village could be such a fulfilling task. Less automation and more human labour would increase probably the efficiency and definitely the feasibility of the project considerably.

-*1)- Of course it depends on how efficiency is defined. If it is production output per hour of human labour then automation is more efficient. if it is production output per necessary amount of machinery, or per capital invested in machinery, or per hours of development of machinery, or per energy consumption then automation is less efficient.

Underestimated Agriculture
The main goal of the project is self-supplying (85%) a village (660 people) with what they need for a reasonably comfortable life. To achieve that, infrastructure and consumables are required. The infrastructure (houses, machines, etc.) need only to be built once and then maintained and repaired. The much more important task is the steady provision of consumables like energy, clean water, food in sufficient diversity and quality, clothing etc. The main focus of the book seems to be on the infrastructure and the machinery to reproduce it. Only little is said about the provision of consumables (most about energy). E.g. I miss more details about agriculture and food conservation and storage. This should not be underestimated in terms of technologies, energy consumption, irrigation, fertilizing, crop protection against pests, seed breeding. Putting a few potatoes in the ground each spring will not do the job. There is nothing about producing animal proteins (milk, eggs, meat or equivalent substitutes) which are essential for human health. Of course they are needed in lower quantity than we are presently used to consume in the western world. But nevertheless.

Design is the real Challenge
Then I miss some attempt to design at least one sample equipment which is able to produce a useful thing AND is reproducible within the village to 85%. To me this seems the core of the real challenge: the design of the equipment such that it will serve its purpose AND it will be able to be reproduced by a 660-person-village. Reproduction of the present designs of tractors, harvesters or sawmills etc. in the village would by far not be possible because of the high number of different raw materials used, the huge number of different parts created by a large number of different processes provided by suppliers and their suppliers etc. To self-reproduce such a machine you would have to also reproduce a good part of the whole industry of today. This is obviously not possible or reasonable for a 660-person-village. To come closer to the feasibility of reproduction the design of e.g. a tractor has to be changed fundamentally to become much easier to reproduce AND still serve its purpose.
First the number of materials used must be dramatically reduced and limited to those available at the location of the village. Another village with different natural resources might have to use a very different design of such a tractor and its reproduction facilities. Then the number of different parts and manufacturing processes must be dramatically reduced. Then the complexity of the parts and the processes must be reduced. And last but not least the design is required to be able to be automatically produced, assembled, maintained, repaired, disassembled and recycled (why all of this automatically?). This probably means a complete and fundamental redesign not only of the tractor but also of the reproduction facilities (machines) by substituting most established designs and processes with new ones.
This and not the lack of SE is the main reason why humanity has so far never succeeded in creating a system with high let alone full level of self reproduction. System Engineering alone can not perform this. Only a complete redesign by forgetting almost every known design today might be able to achieve the goal. This means also that the products (houses, house-hold equipment etc.) might look very different to what we are used to today. And perhaps if some future villagers knew today how that new habitat would eventually look like then they might decide not to participate in the first place...

Since there has never ever a self-reproducing system been built, I recommend to start much smaller. E.g. just try to plan and develop something as simple as a table spoon for 85% self-reproduction. Yes the spoon is no system but just one part. However, its reproduction machinery which has to reproduce itself as well is already a big challenge. Demonstrate that it can be done within a village of 660 people and 300 hectares of land. Learn from the process and apply the lessons learned to the next more complex product. A part of the spoon machinery can be either reused as is or be generalised for more universal utility. But much new equipment will have to be developed.
Based on just private initiative and funding it might take one or two generations until a Mature Factory supplying a village by 85% can be developed. Only in case of massive investments either by BIG money or by BIG open source volunteer participation it might be done in one or two decades (compare Wikipedia). I would be happy if someone can prove me wrong and it turned out much easier :-)

Enough Land for local natural Resources?
The book budgets 300 hectares of land for 660 villagers to live on and from. I don't know if this is really sufficient. I have no facts to support or question this budget. But let us think what this land has to provide. Construction material for housing of 660 people. Mining of the most used metals. According to a diagram in the book out of 1000kg of rock 50 grams of iron can be expected to be gained. Hence for 1 kg of iron 20 metric tons of rock need to be processed. If I think of all the iron in that machinery: it will require a LOT of rock and energy. Surface or ground water for drinking, washing, cleaning, crop irrigation. Sufficient area for agriculture of diverse food types. Area for living space. Area for solar energy conversion. Area for wood production. Area for production sites. Storage areas. Agricultural area with oilseeds for bio-diesel, lubricants, soap, hydraulic oil, edible vegetable oil. Agricultural area for live stock fodder. Area for fibre plants for clothing. This looks like needing a more detailed budget with justifications. This alone is not so easy.

I am very thrilled about the thought of systems capable of a high level of self-reproduction. But I also see that the challenges are bigger than what a number of intelligent Systems Engineering Diagrams might make us believe. But that is no reason not to try :-)