This was the one reason I didn't buy a filco camo. I liked the media keys, but I use my left windows key all day long.
My solution: buy a regular filco, and bought some stock filco camo keys from someone in the classified section. I just used a simple autohotkey script to make the FN key (which is actually placed where the appskey should be on the right side of the keyboard) + Function key map to the respective media function. Works like a charm.
The FN key on that (and almost all other) boards are hardware-layer, meaning you can't actually access/remap the key using software. You will have to cut traces/rewire as suggested if you actually want to do it that way.
IMO, if you want the filco camo looks with the left windows key, just buy a filco camo case/keycaps from someone, and put them on a regular filco board.
Good luck.