Current situation with MakeUp Ultra Fast v.8.9f on Extreme+ ... there's a break in the black-stained glass block roof:

What it should look like (Shrimple v0.11), at least for the existence of that black-stained glass block roof ... Shrimple is buggy in other aspects:

Just asking for correctness here ... and it looks like a bug.

Mods:

Fabric 0.15.11 for Minecraft 1.19.4
Fabric API 0.87.2
Iris 1.6.11
Sodium 0.4.10 build 24
Indium 1.0.19
Continuity 3.0.0 beta 5
Puzzle 1.5.0

I've deleted my previous comment. I think I now understand the problem you're mentioning:

There are some glass blocks that make some transparent blocks behind them disappear. Is that it?

I'm afraid that if this is the case, I can't resolve it with the shader. It's a mechanism inherent to the way Minecraft/Sodium/Iris blocks or displays objects that are behind others.

If it's what I think it is, you'll notice that the objects "disappear" even without using shaders. The use of the shader just makes it more evident.

There are some glass blocks that make some transparent blocks behind them disappear. Is that it?

Glass panes but yes that's basically it.

If it's what I think it is, you'll notice that the objects "disappear" even without using shaders.

This is probably a Sodium problem, see CaffeineMC/sodium#2590.

Fixed in Sodium 0.6.