Do you think there would be too much stress on the scupper holes of I were to rig up a seat using some poles down in the scupper holes for support?

By guess: If you are under 180lbs, should be OK.

I wouldn't do that

I'm with Hooked. Buy 6' of 2x6 redwood construction grade lumber and take a grinder with a flap wheel to it. Shape it to fit the 2 depressions, and then mount your seat on top of them. It might take a little time to get it right, but when you're done, you will have a solid base and you won't damage your kayak. I'm planning to build a base for an elevated seat for Daveg99, but he hasn't brought it to me yet.

Worst case you void warranty, cause leak in scupper that fills hull, you dump your kayak and loose all your fishing gear. If you can handle that ... go for it!