"the most we can do is just change the clouds to grey "
This is exactly what is needed for our eyes. This is all that is needed.
Thunder clouds might be cool though.
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What ever happened to common sense? If the clouds are too bright look away or close your eyes. I sometimes play in the dark and when nexting I close my eyes. The change in brightness from clouds to the next base is obvious to detect even through eyelids.
It does hurt my eyes if something bright suddenly flashes into my eyes once I've stayed in the dark for a long time. But the longer the bright light is turned on, I slowly get used to it (even at night) so the bright white clouds during the game's loading phase (visiting the War Map, visiting other players' bases, nexting, etc.) doesn't hurt my eyes anymore.