Yep, done it - with roughly a 50% success rate! I had to touch in the Dull Red of the roundels on the Mustang fuselage, as the black stripe showed through one half of the central circle; wasn't a problem, but could be a tad tricky on code letters.
One possible solution is to trace the outlines of the decals onto the stripes, and then paint the required areas i, for example, white, then place the decals. Alternatively, you can overpaint the decals in the same colour(s) before applying. Just give them a quick coat of Future, or similar clear coat, before using. This will lessen the chances of the paint cracking when the decal is slid off the backing paper. It works well, you just need to be a little careful during handling.