Assuming the patch is smooth and taunt applying second color trim with the same covering material (Monocoat is my preferred product) is much easier and works quite well if you vent the base covering.
On occasion for this I use a dedicated tool called a woodpecker but you can also do the same just by using a dressmakers pin (very thin) and making many tiny pin holes on the entire area where the second trim piece is to be applied. It makes no difference whether or not it is over balsa or open bays and it works equally well over both.
That's a really interesting idea; thanks! I've always cut away the covering on the bottom layer except for about a quarter inch border. Your method would achieve the same result but ought to be easier because the edges of the bottom layer wouldn't sag. (That's for open bays; over wood, they ought to be about the same, I think.