Take em off!
Both pieces, I've relocated many many customer's tool pouches either on the backside of the footwell(on either side) or take the owners manual out of the seat and throw it in there. One customer cut his seat out. I don't bother, can't feel it when riding anyways.
I also too kthe plastic from the righthand side out too. Ziptied the harness and wiring to the frame, up and out of the way of the engine and pipe.