Steps to reproduce

1. Create a custom block with a custom geometry and textures such that you can see through parts of it. Or use test.mcpack, which contains a pack with a custom block named my_test:my_block.
2. Create a world with Holiday Creator experimental features enabled and enabled the behavior pack with the custom block.
3. Make a flat 7 x 7 pool of water source blocks.
4. Place a 5 x 5 platform of glass or leaves blocks over the center of the water.
5. Replace the 5 x 5 glass platform with custom blocks.

Expected result

You can see the top of the water through the custom blocks.

Actual result

You see the top of the water in step (3), but in step (4) the center 3 x 3 section of water does not render.

Analysis

The water surface not rendering is the same behavior described in MCPE-76109, however, in vanilla this only occurs with full, solid, opaque blocks and mob spawners, not with glass or leaves as shown by step (3) above. The intuitively expected behavior for custom geometry is that water rendering would react the same way as it does to glass. In other words, the game should assume that blocks with custom geometry would not be opaque full cubes.

The behavior of water rendering here occurs regardless of render_method used within the material_instances component. My guess is that it may be partly based on the block's server-side properties derived from its materialType (e.g. glass, wood, stone, metal, etc.), which it seems cannot be changed for custom blocks.

Strangely, the custom block in the attached pack is also impacted by MCPE-124841, so from far away you can see neither the block nor the water under it. Aside from MCPE-76109 and MCPE-124841 being problems in their own right, it is definitely unexpected for the same block to trigger both behaviors.