You will notice that the vanilla pneumatic door, aka Mechanized Airlock, (and same for manual pneumatic door) is constructed with


instead of


I have created a mod with a "custom prenumatic door" by just copying the vanilla code and changing that one setting gave me the same "visual bug" you're having. See bellow:

https://imgur.com/a/lMiLAvQ

I don't believe it is just visual, there might be no immediate or obvious sideeffects of doing it this way, but as we all can see it is not working as we expect it.

My next step would be to decompile and recompile your mod to verify this works. If it does I'll stick to using this private version of your mod it in case it is not officially fixed. Otherwise the mod works very well and I like it. Good job.

Edit: I've recreated your mod and it seems that I stand corrected, it seems that the "shadow" from water is for whatever reason drawn on top of the door instead "inside" it. I say this because I have not noticed the vanilla doors had the same shadow but only on the inside when opening or closing. It might be something with the animation order but I'm not sure how you control that. Although my solution kind of looks nicer and the missing shadow is less of an eyesore, it's still not ideal though.

Doors opening below (from left to right: your door, then my recreated door, vanilla door):

https://imgur.com/MjX3zZd

But also water does not animate on top of my door when flowing through:

https://imgur.com/abfluzY

So my solution was misleading. Back to the drawing board.