The water cannot pass through the transparent box after being refreshed by the sponge.

Water only flows through transparent block if it is a water source. The sponge probably removed the water source on the trapdoors. Try using a water bucket on the trapdoors.

Thank you for your report!
However, this issue is Working as Intended.

You can place water in things like trapdoors (non full blocks) or place trapdoors in a water source-block and they will not remove the water source-block. Both will occupy the same space (water source and trapdoor).

Water will not automatically create source blocks in a occupied space. This is in place to prevent breaking worlds or contraptions.

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Well seeing as this works in Java, but not bedrock, then I'm bringing this up as a parity issue. If this works as intended then it should work like this for Java too.