In my experience you can spot spray the gloss, decal, and then the flat will cover the sheen.
I'll warn you that on my last big model plane a 1/72 A-400 the decals silvered badly even with two coats of MM gloss laquer (I had to painstakingly cut out the silvering and gloss over which worked pretty well) , so I'm contemplating using the alclad aqua-2 gloss next time.
You can also spot brush on Future, which would probably eliminate the problem I had, then MM flat laquer as final coats.
One thing to remember when spot brushing is that gloss can slightly change the color variation of the paint, and make it darker. So this would be your decision as to whether you do the whole model or not