Hey Erik,
the scotty flush mount on mine has a recess into the hull (10 cm approx) but would probably only get a minimal amount of water in rough as it's a pretty snug fit when locked into place. Yours would sit pretty high in the middle point of the prowler too out of the waves yeah?  It also has a cap that goes over the top when you take the holder out.

On another note had it about a year and no rust on the stainless at all and the baitholder strap looks in good nick. The baitholder style has worked well for spinning and overhead reels although it's within arms reach on the right side, not in the middle as you plan which may make the strap a little tricky to get off.

Cheers

See I actually quite like the normal scotty holder because it keeps my reel higher up and away from most hull splashes while I'm paddling. Not much better in the surf but I de-rig before all surf.

There is the advantage of price and less wind drag with the flush mounted regular style rod holders but when you're my size thats all out the window.

I mainly use the scotty because I do like having the ability to adjust the angles of the rod.

As Bush & Badfish have said...

that was my concern with the prowler  NM