I have not checked to see if I've experienced this bug on earlier snapshots but today I noticed that all maps I craft seem to have these chunk tearing issues. This is not reflective of whats in the overworld. I can confirm that this issue is linked the the problem of rain clipping through some blocks in the overworld and can even be seen clipping in caves. I believe a rain glitch was patched in a previous version but this bug seems to be a separate issue.