The fog in the nether is too dark, but it renders as its normal color for a brief instant whenever the weather changes to or from clear. This is much more pronounced in soul sand valleys than in nether wastes; I haven’t tested with the other biomes yet.
See attached video for reproduction steps (public viewers will need to use the logged-out view due to META-212).
I would not be surprised if this is system-dependent.
Suggested approach
Making it so each dimension has a flag for whether or not weather is enabled is probably the best solution. While you’re at it, consider making weather work on a per-dimension basis and make /weather dimension-dependent (the command would fail if the dimension does not have weather).
Resolving as fixed since I can no longer reproduce in 25w45a.