It seems like you should be able to add the Bubble column's block ID to the shader's block.properties file after it says "block.31000=water flowing_water". I haven't tested it, but theoretically it should work.

Not sure I can fix this, as I don't know how to indicate to shaders that my bubble column block should be rendered as water.

I have pushed a fix for this to the main branch but it's not yet released. The fix requires hacking OptiFine in multiple ways, and will need to be tested in modpacks to ensure it does not cause unexpected behavior.