Have done a couple in RS frames now to is you can do it powder coat the pipe and the low pros separately or product with the pipe with the low pros on it but you do need to take off the locking nuts and put a stainless steel not on otherwise the robber or whatever material makes not locking nut will melt and be essentially useless
Haven't had any issue with the frame it's been several years I did a hammer coat so even if that nicked up it's still look brand-new happy with it
As for masking they do have tape I don't see any reason to plug holes you can just drill or screen right through them
My frame is not powder coated but I am a Glazier by trade and work with powder coated aluminum all the time. I will chime in a say that even though powder coated materials are more durable than paint it is not that hard to scratch it especially while putting a dry box into a bay on your frame. How long it holds up will mostly depend on how you treat it.