Installing with RubidiumExtra will cause the barrel with color to display abnormally

You will need to report this to them as sophisticated just uses regular coloring of blocks that's supported by vanilla.

this seems to be the exact same issue that rubidium extras causes to another mod txnimc/MagnesiumExtras#34

Incidentally, this issue arose after upgrading SophisticatedStorage, which was not an issue in older versions

Sure, but I don't think I have done anything so substantial there (other than adding layer that displays lock) and it works without rubidium extras. So given that I believe I am not doing anything wrong until they can tell me otherwise there's nothing to fix in sophisticated storage.

And actually I seem to have been looking at incorrect rubidium extra project and there's already a bug for exactly this on the one that I guess you use dima-dencep/rubidium-extra#29

Well, then wait for the other side to solve it, anyway, does not affect the normal use