These are actually 2 problems interfering each other.
When a group of transparent blocks merges with solid blocks e.g. leaves merge with grass blocks.
You will be able to see through blocks(from the transparent side) like an X-ray. (problem 1)
This happens inconsistently and I cannot figure out which kind of blocks will merge with each others. (problem 2)

Please include the version of nocubes you are using and share a picture of problem 1.

I do not understand what you mean by problem 2. NoCubes merges blocks based on its configuration, if you want to change which if a block is merged or not, look at it in-game and press n. Does this fix your issue?

After futher investigation, I've figured out that ModernFix is causing this issue

I would assume that the transparent blocks will merge into a mesh and the solid blocks will merge into the other mesh.
ModernFix ruined that and now the two group of mesh is unpredictable
Versions:
modernfix-forge-5.7.5+mc1.20.1.jar
NoCubes-1.20.1-0.5.0-dev-b81a6c5.jar