As long as you have good clean steel to weld to and prep the surface correctly, I would have the guy mig weld the new floor pans in place. Flux Core (simplest process) will do well with a series of short fillet welds.

You can use a seam sealer between the new and old panels with the new being on the outside and a 2 inch wide lap joint, if possible.

Then POR the inside/outside and should work.

The key is to cut out all the rot and get to clean metal, use POR Metal Prep and make sure the weld area is clean. You can pre paint within 1 1/2 inches of the weld area without worryiong about damage and can repaint after if needed.

I have used the Lincoln 135 Welder sold at Home Despot to do similar sheet metal welding. just do short, small welds to keep the heat down.