Depends on the powder coater...
I've seen some powdercoated rails without probs... some powdercoated with. I personally experienced rail failure that was caused by powdercoating.
It is more about the temp-control and bake-time than "powder coat" in general.
400 degrees, typical pow coat temp, believe it or not is the temp at which the 7129 alloy is heat treated at... you can "over age" the heat treat and make them more easy to bend.
BUT... if you have a top notch coater that can use a 350 bake temp and low temp powders without a long time in the oven... and use good quality powders... you will be just fine.
The commercial volume shop that is putting your high-tech-alloy snowmobile rails in the oven with the fence posts from the highway commission, or steel machine parts will cause you trouble.
This is, I believe, the reason that some people have no problems and others have big problems with the pow coat and structural strength.
The process .... prep is everything. Do not allow a "Heat soak" or "bake off" in the oven to clean them.
Good Idea to clean them yourself before taking them in... takes that out of the equation and may save you some $$.