I have painted the inside of my cowling a dark brown (nearly black) - but the reason for that is solely that because it has a 049 engine in it, I've had to cut large holes through it for the prop, starter and piston heads to go through, so you could easily see the inside of the cowling around the engine.
As for roughing up - yes
I made the mistake of not doing so for the inside of the cowling and it took me 4 coats just to get paint on it all, and to stop it "balling" up. A light sanding on the surface of the engine exhausts made the (same) paint adhere MUCH
MUCH better - one coat was enough!
As for the enamel deforming the cowling, I doubt it - I painted Airfix 1:72 scale models for years with enamels, and they were always fine - no matter how thin the plastic parts. Careful with the enamel thinners / white spirit / adhesive tho, as they will cause you problems on the thin plastic. Enamels are also heavier than acrylics, so if you're going for a really light aircraft avoid them if possible.