VTX w/ Standing Water in V-drive Compartment

Hey guys and gals,
I'm a newbie here, so be easy. I am looking at purchasing a 2007 Wakesetter VTX and I went to the dealership today to give it a good look over. The overall boat was clean, needs a good detail but nothing that could not fix cosmetically. While I was inspecting I opened the rear center seat hatch and took out the pan below to view the v-drive compartment and to my surprise it had almost 6" of standing water in it. Up about 4" onto the V-drive case. So I then opened the small (1'x1') compartment hatch right in the center of the boat (next to the drivers seat) and same thing! The hard ballast tank in there and the two ballast pumps were in approx 7" of standing water. There was also water puddles in some pans under seats. It has rained very hard here lately so I'm sure it collected rain water because the boat is only on a yard trailer which is not high enough in the front. The plug was out but only minimal drainage when the boat was rocked.

I then inspected the engine compartment and everything looked fine, just about 1" or so of water down on the hull bottom but nothing was submersed.

So to my question. Is this bad, will it reek havoc on the electrical system for the ballast wiring and such, could it effect the V-drive housing, please elaborate if you can.

The dealer said its no big deal at all, that its fine to have that but it needed to be drained before the boat is started and run? I'm looking for a non-dealer opinion on this one if you can believe that.

Please help if you can?

Thanks in advance!