I think they're distinct enough tags not to require a merging / synonyming (if that's a word)
For example, some questions tagged color that wouldn't make sense to be color-scheme are:
How to interpret wcag2.0 guidelines on contrast for buttons and icons
Correction in color model
Intuitive colour pickers for non-expert users?
Really, I think color-scheme ...
Retagging posts has always bumped them up the active questions list, it's not a new feature.
To be honest I think I disagree with you that it's undesirable.
Retagging questions should bump them up to the top of the page. The reason for retagging questions is because they have the wrong tags in the first place. If a question has been tagged incorrectly ...