I also wanted to start with a solid foundation, so I ripped the rubber floor up.
I have a 1/16" steel floor in mine, so I wanted to see what rust damage there was.
Fortunately, there was not much rust and only thru in two small places less than 3/8" diameter, so after I cleaned, treated the rust and primed it with 2 part epoxy primer, I patched those and all the seat mount and screw holes with galvanized tin caps held down with butyl caulk.
There was a little caulk sticking out the sides of a few, but that was trimmed off with a wood chisel.
This made for a relatively flat and well sealed floor.
I have carpet everywhere except the bath where I used vinyl tile.
The vinyl is pretty flat with no padding, but is covered with a rug!
If I was going to use tile or sheet vinyl on a whole bus with a steel floor, I would probably install a subfloor or float out the seams with bondo or something to make it as flat as possible.