The water doesn't seem to render behind stained glass on schematics. Changing the render depth doesn't seem to do anything either.
However, if the glass and water is spawned in Mine-Imator as blocks, the water seems to be visible, but the blocks need render depth set to at least 2.
https://imgur.com/a/OI6ZpRE
Here are the projects if you want to test this yourself:
https://drive.google.com/file/d/1Yu33XS0QxHGfPb5lyLKvmiWBXW4ZEXSP/view?usp=sharing
Cheers.