I don't think I've ever sprayed over powder coating before, so I can't offer any advice there. You would think they'd get along okay though. (?)

The enclosures I've refinished (just for a custom look, like the Caline pedals) I stripped bare and primed. Then just used duplicolor for base coat. I prefer the Septone Clear, so that's what I used. I think I've used White Knight Clear Acrylic on pedals too. Haven't had issues with either of those adhering.

All the other pedal enclosures I've done have been bare metal off the shelf.

Maybe Andy40 will pop in with advice.