Playing with a test world using only GT++ (pre-4), Advanced Rocketry (1.2.5-63), and their dependencies, there are large patches of Dark World biome generating on the Moon. It doesn't appear to be an ID conflict.

Could be either a biome or dimension ID conflict..
Otherwise, I have no idea.

I meant it doesn't appear to be a biome ID conflict.

Did this ever continue happening?

I'll be happy to investigate, otherwise I'll close this issue in a week.

Changing the biome ids appears to have fixed the problem for now, which puzzles me because they didn't overlap in the first place.

This issue is still occurring as of GT++ 1.7.02.09 and AR 1.7.10 1.4.0-020. Also GT++ is causing water to generate all over the Moon as if it were the Toxic Everglades, which I don't think was the case before.

Is it possible for the user to disable the dark world module?

The issue exists on ARs side from my first guess, as No other mod misuses the Everglades biome.

Did you try change the dimension or biome ID?