I am aware these problems may be my own fault for not having proper settings/mods installed.

I started a new game with BA+MadClown+AAI mods. So far things have gone smoothly, but I've come into two progression issues:

Science-1 required copper and iron ore and was required to unlock ore sorter. With BA ores, my only way to get around this was a console command to give me a single ore sorting facility then I could produce the ore needed to unlock ore sorter recipe.

Around the time of needing science-10, I noticed there was no recipe for normal chemical plants. Angels chemical plant was replaced by science assembling machine with none of the usual chemical recipes. There was a disabled recipe for 'chemical-plant' but enabling it didn't help as it had 'angels-chemical-plant' as a product so also produced science assembling machine.

The second issue I solved by making a small mod that changed the result of the 'chemical-plant' recipe back to 'chemical-plant' instead of 'angels-chemical-plant'. (And the same for chemical-plant-2, etc.). But this is probably a hack specific to my mod set.