I have yet to actually beat the game, but this playthrough I decided on going with a central logistics hub and modular factories. All goods flow into and out of the hub. Blueprints for rail bridges have been essential, but modularizing the factories has really helped cut down on the complexity. Most primary manufacturing is done on site at the point of resources, and further manufacturing is being done near the hub. If I can take advantage of a resource while making higher tier goods, I will. I also have made sure to integrate a hypertube network into the rail bridges, which has really helped with getting around. I'll sometimes add "booster" sections in the runs to speed things up.
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Oh god, that changes so much.
I've built a caterium computer factory with 200+ machines total and I used 4 different blueprints for it. It was still a lot of work because each blueprint had like 3 connection points that needed to be connected manually. Very tedious, will not try again.