I have had problems with tape pulling up the Alclad, and I don't like the effect the glosscoat gives. So I always do any color stuff before I do the Alclad. I do the lighter colors even before the black undercoat, then mask. I often do dark colors on top of the black, then mask those off. The Alclad operation is then the last painting.
Also, another option is to make homemade inkjet decals for color stripes. I have done this at times when a painted stripe is too much work.