My friend and I routinely have conversations about factory design.
His ideal factory ships every ore in its raw state to a single building, which can then move the ore to different floors/sections for processing. He goes further than most and separates each product into its own "room", so all steel bars are made in one room then shipped to the steel beam and steel pipe rooms. Importantly the factory should be designed so that you can "infinitely" expand a room if you need more of that resource.
I prefer what I call "microfactories", where each component is created in a small, independent factory and the result is shipped to a main repository for builder use and for the space elevator construction. If you need modular frames, for example, you would find a group of ores and build a small factory on it and build every sub-component you can in it. Ideally, it would not rely on any other microfactory's outputs, but sometimes that's easier said than done. Often I will have a small cluster of microfactories all dedicated to shipping their output to a final microfactory for processing.
So what do you all use?
Note: He claims his design is more analogous to microservices (from software architecture) than mine, and that mine is something apparently called "pirate architecture". I think he's out of his mind on that one.
I suppose I'd call what I do a "mill and factory" architecture which seems to be similar to yours.
I'll find a resource site - take for example the infamous now-nerfed cliff in the west Northern Forest, and I'll put an iron mill there that does everything from smelting up to, say, reinforced plates or modular frames. Same with steel mills, refineries etc.
These will feed a small number of major centralized factories. One that I'm in the process of building the 1.0 version of now is always located in the southern Rocky Desert that I call the Desert Automated Manufacturing Node...In my Update 5 playthrough I amused myself by giving all my facilities rude names with technical sounding acronyms, and the DAMN stuck. I still call it that. It's the mid-game factory, it makes motors, crystal oscillators, heavy mod frames, circuit boards, AI limiters, high-speed connectors, computers and supercomputers. Big factory that takes up most of the big empty section of the biome. It, along with the late game (radio control units, turbomotors etc.) and now the quantum process factories will ship goods to the Project Assembly Tower where the space elevator lives.
My nuclear power plant is as self-contained as possible; I don't like pulling from main production to feed power so it gets a whole weird mishmash factory unto itself. This ended up being the only successful sushi belt in my last playthrough, as I needed several kinds of things in fairly small amounts.