With SH3Cmdr R2.5, I can pretty close to boldly state that any aspect of SH3 can be randomised.
Your task could be achieved one of two ways:
1. If the clouds are stored in image files, use the Random folder structure. Images shouldn't clash with any mod, but I would naively suspect that there may need to be some consistency in image size and content - and this may be linked to other environment files. But hey, I really have no idea other than it could be done.
2. If the clouds are defined by data file settings, use the new "Randomised Events" feature. gouldjg is successfully using it with his Hollywood Chaos mod, and it's the way Hemisent's Thermal Layers mod has been implemented. Less likelyhood of conflict, but even if so, easier likelyhood of rectifying.