After the removal of the quality in efficiency modules.. A way to solve these problems could be to make new variants of modules who are "mixed".
So there could be "raw modules" like they are here now and "mixed modules" where you combine two modules and get the combined effect (or - if too strong - you get two modules which have half of the combined effect)
This way the players could choose which variants they wanna use.

I thought also about a mixed one. I a recent Minecraft pack I played was an everything upgrade for each Tier.
U had to craft all Module 1 together to get a Mixed 1 with all the effects. Maybe this is an idea.

oh yeah, i did see your last post about the efficiency things, honestly didnt think of that being an issue - that is on me
(and i just got rid of it completely from eff modules as a quick fix)

the main reason why i added it, is because speeds decrease quality and having something else give a slight boost (because something something, more efficient) sounded like An Idea that i liked - i will probably add it back as a mod setting though

and maybe? i do like the inherent idea, but i personally feel like it is out of scope for MOAR modules specifically - however i wouldnt be against putting it in its own addon mod for MM :]

I would have another idea, what about you hide the extra quality behind a research. that way everyone can decide not to research it or do it when feeling ready. While it is bothering in the early game, it definitely is possible to design a base fully around it.

oh and another idea if u scale the numbers a bit lower on the efficiency it would be possible to counter it with speed.
example: 2 efficiency module 1 + speed 1 = 0 quality
this wasnt possible for me because it was 0.7 and not 0.5 quality.

this might open up a 2nd level to this mod to make ppl mix modules since we get 3 bonus tiers on top, this should not hurt. even combine able that they only gain quality when the quality research was done