Right, thats only part of it, as mentioned very few of those buildings actually make use of that mechanic. and thus it comes very unexpectedly for some recipes.
Considering the progression is from 2 to 4 to 6 items for all of them (and 4 is already huge) you "opt-out" of this mechanic quickly at tier 2 machines... if ingredient limits are something to keep in mind, the progression would need to be slower instead (like they were in the base-game)
Since you mentioned modding it back in, it could be a settings flag? As I'd suggested, fixing the tech tree to account for this would be a decent fix as well.