I found two issues with a single datapack. I don't believe they are related so this one is about how this datapack causes the overworld sky to be added to the nether. The only thing which was changed in the datapack is the fact that logicalHeight is not 256 when it was 128 before.

This bug report is about the sky and not the fact that changing logicalHeight does not work. That is bug report MC-197338

What should happen:
1. Nether should not have overworld sky