It seems rain can go through blocks underground. It is inconsistent with where it appears to come through, but I have noticed it does not seem to come through blocks placed by me (Wood cobblestone etc)
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This was fixed in 20w18a, however worlds opened in 20w17a will remain affected by this issue. You need to optimize the world and erase its cache. For instructions on how to do that, please look at the instructions from MC-179845.
Duplicate of MC-179845