As far as I have tested, following mods should not include quality:
- Max Rate Calculator
- Ore Eraser
(Both mods only have an UI button which somehow get quality modifiers)

Something from the Logistics Train Network mod gets quality (called entity-name.logistic-train-stop-lamp-control) which it should not.

Also the modules from Advanced Modules do not get better when making the better qualities of them.

MRC and OE use selection tools. Do these appear somewhere other than when using cheat/editor and/or cause issues?
Same question for the LTN thing. Do they appear in weird places or cause issues?
If not, then it's just a minor issue to reduce prototype count. Let me know.

As for the advanced modules, the normal modules should get bonuses i.e. the normal speed/productivity/effectivity, at higher tiers. Let me know if they don't.
The "god", "pure-productivity", etc have different categories so it's not obvious which effect is the "primary" that should be boosted.
I can make it work by "boost the good, and ignore the bad" - that should work for this mod.

The Ore eraser one is a bug in that mod. They should have set the flag "only-in-cursor" for the eraser. I've added a filter for such items for MRC for next version.

The LTN stuff is buildings with health, so I don't want to filter them.

The module thing will be fixed for next version.

The MRC, OE and LTN Items only appear in creative chests. It would just lower the recipe count. So no visual appearence in a normal game.

Normal Modules work fine. its only the modded ones that did not work.

"The LTN stuff is buildings with health, so I don't want to filter them."
I dont think they are because they dont even have proper names. Probably some placeholder or indestructible items that get placed inside/near the normal LTN Stations but I am not sure. They also dont have an icon so yeah...