My only concern with something like that is its going to mess up the outer skin
Get a piece of plywood larger than the window opening. Drill a few holes within the area you are going to cut out. Put bolts in those hole, and "clamp" the plywood to the outer skin.
I would think this would hold the metal flat and you should be able to even use a recip saw on it.
Shouldn't. Especially if you tape it.
This thing leaves a really smooth cut.
Chris
Did you get a milwaukee M18 metal cutting saw? We have one that cuts strut and other metal like butter.