Thanks for the very interesting mod!
Early game is mostly "working out how to do stuff" so it's a slow start. Mid-game is lots of "scaling stuff up" together with new recipes...
By the early mid game there are a lot of complex recipes (many inputs). Especially the electronics recipes leading up to bots. Automating the science is easy enough, but automating production of belts, factories, inserters, turbines and especially bots gets so complex.
I'm really not a fan of "everything is an upgrade from the previous tech level"; it just feels like making recipes more complex for no good reason. Nullius also makes it hard to segregate the factory into different components since so many resources are used all over the place.
Of course once logistics systems have been researched a lot of that complexity in the meta-factory "mall" is easy to deal with (especially since a lot of it is low volume items).
In the end I automated belts, inserts and part of the electronics and turbines before logistic systems, but gave up getting these things properly automated (or doing any automation of assemblers or miners). My early "mall" was mostly for belts + metals.