I assume you’re talking about the pad on the ‘T’. That being the case, I assume it’s to provide some support and maybe eliminate some squeaks.
IIRC, there is a triangular pad that sits on the vertex of the legs of the frame in front of the motor. That is for the same reason but is more obviously useful.
I don’t think I replaced all of the jute padding except the triangular piece I just mentioned with closed cell neoprene foam. I got mine from a local rubber dealer (IIRC 3/8” thick) but r.d. enterprises also sells that or similar.
As for painting the inside of the frame, I probably sprayed it as best I could. Maybe you could find a small spray gun that you can operate while you hold it inside the frame. You might check out and undercoating outfit. And then there’s this method: in one of my engineering classes when we were learning about corrosion resistance methods like material selection, plating, painting, a test question was how to protect the inside of fabricated hollow beam 12’ long. A lot of us tried to come up with some clever, high tech way to do it but the answer was to prop up the beam on one end and pour paint down the inside!