Yes you can remove the wheel. I think also the existing cover will happily become your new base floor when placed in below the upper support brackets.
I went a different route. I need a rubber spare as I tow. I also carry a full set of tools, diagnostic kit, modicum of emergency (get me out of here) spares/things. If you remove the polystyrene under floor filler then this opens up a much bigger storage area. I just emptied my tool box and put all the tools into several tools roll pouches etc. Also put slim height hobby storage boxes on top of the spare wheel as there is 3 inch+ gap between the wheel and the floor divider.
Suggest you experiment before finalising your decision unless you just want big square box, luggage case space etc.