I've got several powdercoated Pack Cat frames. They don't mark the inflatable tubes like aluminum and galvanised steel.
Straps do rub or gouge off the coating to some extent. Also impacts seem to crack through it at the end of framebars, and you can get nasty corrosion underneath, especially if you use the boat in saltwater.
Regular inspection and maintenance is the best cure for the problems, which are rather few.
I've got a custom-built powder-coated frame... for the extra cost, and the benefits of having it, it is pretty much worth it. Just be aware if you ever have to get a part fixed (i.e welded) on it, the welder has to burn off some of the coating. We just had major issues with the builder of the frame not wanting to pay for a re-powdercoat after having to re-weld some joints that were breaking.
You'll probably get lots of compliments on a nice frame for a year or so, or at least until it gets beat up. You may get a little color rubbing off on the rubber at certain contact points. Be careful about major scratches and dings, too. Like Chip said, the coating may flake from a ding.
If it's Al find someone who can annodize it. Much better than powder coating since it is a conversion coating, not something applied ot the surface. It won't flake, won't rub off as easy and should eliminate the black marks.
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