The chip resistance of the powder coat would remain, it's just the paint on top of it that wouldn't have good adhesion that would be the problem.

You could have the powder coater mask the outter surface of the rails that you want to paint, and then do the rest of the frame. Then just do a conventional prep and paint on that outter surface. One other point that hasn't been emphasized, you can't powder coat over polyester filler (bondo), it won't survive the process. As mano says, bring a sample of the paint color you want to use on the outter part to see if the coater can match it, or find out if they have something you can live with and have the paint matched to that.

BTW, if a painter won't pay attention to the details of the frame that you're concerned about, he's probably not the guy to do the rest of the car either. Good paint work depends more on the prep than on the final coats. If he's lazy on one area of detail, he's probably lazy on all of them.