Seats are filled with foam to assist in the tinny being able to acheive neutral bouyancy. That is, when it sinks the whole boat doesn`t go under. As long as you are not removing to much of the foam material and plan to shroud any wiring in case it gets hot and melts the foam you should be ok.

 Yer it will b right it's a pain in the arse though I fitted stereo, speakers, and switch board in mine. There is a support in the middle of the seat which dosnt allow u to pass the wires from one side to the other. Mine has been in for the last couple of years without a problem.... Knock wood. I would give every thing a good spray with inox or something before u seal it away, help prevent corrosion..

Instead of cutting in to the seat why not get a Perspex box made up that sits on the seat and mount your switchboard, sounder, Gps and radio in it

I installed a "glove box" type thingy to my front seat, which in turn weakened the seat and it collapsed when my mate was sitting on it.

Had to get a whole new aluminium seat made up.

 Shit that sounds like a bit of bad luck there pale ale. I thought about the box option but decided down this road as it all sits neatly away in the seat dinghys are small enough without adding extra bulking bits in them.. I put the glove box to in my front seat

Whats going to stop water getting in to the seat?

Regardless of you cutting in to the front or the back there is still going to be water running down the faces at some time and sooner or later you are going to end up with condensation and that means "fungus" growing on all the electrical connections and failure not far down the track.

At least with a box that has a good fitting window you can keep track of what's happening.

 Sikaflex went in and around every nook and cranny. So yer if I ever had to try pull it out it wouldn't b easy.. Lets just hope that's not the case

 How about putting a bit of marine ply in that corner to fill the gap between the seat and transom under the rod holder.

then you can mount some electronics under that, buy a can of soft seal and use vigorously 

Marine ply box with hinged lid maybe ...mount it on top of seat end using those two verticals , switchboard on face with sounder etc on top with small battery inside ..  

 i cut a sqaure out of the seat (top) and mounted my battery in it inside a battery box, master switch on back of seat...put a plate over top to keep weather out...you can get boxes for switch panels from 12v shop i think...put one in my camper trailer...otherwise with good sealing, right wire, and wires protected with wrap i reckon it would be okay....i use battery terminal protective spray on the back of my electrical set ups....dont know what youre running but how bout a tidy ali box with all electrics set up in it with a plug set up to battery...this way when not in use all electronics can be taken out easily for security...seeing the floor ribs maybe you could mount a box on a pedistal type pipe that can rrotate if sun is an issue...just attach a mounting pipe to a floor rib between the front and reaaar seats to the side of choice...have fun fitting out the toys to suit your own personal preferances is enjoyable