On Crucible one of the buildings is supposed to get additional module slots from quality. When your mod is disabled it works perfectly with your mod enabled it doesn't. Is there any way for you to make it so that modded items aren't changed by this mod?

As a temporary fix I have enabled that assemblers are effected by quality. As I don't want this to be true for every building hopefully there's a fix at some point but for the time being at least I can work forward on Crucible.

I hadn't made the kiln on Crucible yet but the same is the case for it.

Sorry for the late response, but I have been considering how I can approach this issue. In the end I decided to treat default values as skipped adjustments.

I was hesitent to add this at first since it would require a guard to be added to every single adjustment point, but I think the extra work is worth it if the end result is flawless. I am currently on the first pass at adding the default value guard to everything, so it will probably be a few days since its a bit more involved and I need to ensure this is fully functional before I push it to release.

several days of attempting different wrappers for ensuring we do not adjust default values, and I did not quite nail it.
I wish I had a simple solution to make this work but everything I came up with just felt off.
The best I can do for now is simply guard the adjustment of quality_affects_module_slots on the assembly machines and foundry. That still leaves the issue of crafting_machine_module_slots_bonus being an adjustment made to the quality prototypes themselves by both this and the mod in question. It is not as easy to set up a guard for this value since its interconnected with 3 other settings as well. I would suggest finding the value they use in their mod by searching for the crafting_machine_module_slots_bonus key.

Overall I just ended up spending too much time on this for now, so when I get more time I can approach this once more.