Why wouldn't it? You're not changing the composition of the metal only puttin' a coating on it. If you somehow manage to improperly coat the metal and trap moisture or other corrosive agents against it, than all bets are off.
Sure it will. Some Sig's and the S&W M&P's are stainless slides with a finish on it. I'm sure there are others out there too I just cant think of them off the top of my head.
The coating should not cause any rust issues over a stainless steel gun.
The coating