The pipe creation seems to be an issue on your end, as I do not create 5 connections. I need the full error code to add a mod that breaks it as a hidden dependency, so my code loads after it.
Part 2 is not hard to fix; it's just not implemented currently in code. My mod is mostly hand-made, so it does not automatically cover new machines unless they have been added. I made it so it's really easy to implement new machinery into the code; practically anyone asking any AI (LLM) to implement their machine can get it running on their own.
Tho, you are mentioning that it just adds more modules.... So, I looked at the code they use and.... uhhh... they deep_copy the vanilla machines and practically everything in the data_updates, while I do my fixes in data_final_updates...
I could theoretically move my changes into data_updates, but there is a chance I will run into issues with other mods that mess with fluid_boxes for one reason or another... I could make it so if this mod is installed, I will also do my changes over machines with their mod tag too... It's just quite annoying...
Does that mod copy every machine in every mod or only vanilla? From what it seems, it just copies assembler types...