Using the checkboxes on the outfitter/companions do absolutely nothing, and when exiting the page, or changing anything, all checkboxes revert to unchecked. On the outfitter this can be resolved by clicking the "Unify Colors" button which forces all armor to unify, but there is no way to unify individual armor pieces. For companions there is no unify colors button so there is absolutely no way to change outfit colors at all.