Don't they use paraffin wax for undercoatings?
It doesn't seem to last very long.

The bedliner might actually be a good idea if implemented correctly.
Powdercoating the frame and such will give you the corrosion protection needed, and the bedliner will provide an added layer of "cushion" to keep rocks and such from damaging the powdercoating as well as helping to seal the frame from the elements.
If a brush on was used and the liner took some damage on the last ride, you could simply brush some more on and you're good to go.
I suppose standard paint on the frame would be fine too, just as long as the frame is sealed from moisture.
Won't be as tough as PC+liner, but my guess is that it would be tougher than PC alone.
With brush on liner, you can elect to only use it on high scuff areas, coat the entire frame and skip the mounting points, or just coat the visible areas of the frame (no sense in coating the part behind the radiator, right?).
A-arms and swingarm would be another good place for it.

Keep in mind that the liner adheres best to a rough surface, so if you've got chrome a-arms then it probably won't last very long at all.
Bare metal and roughened paint seem to adhere about the same, though you don't have the benefit of corrosion protection with bare metal.