From what I understand, you can use the in-game configuration and not use the SST software, however I don't believe there is a way to get the game to recognize the different mode buttons. It would be nice if there was a way for it to see button A as A1 in mode one A2 in mode 2 etc.
I currently use an x45 and since I do have the same button doing different things in different modes, I've stuck with the SST software for now. I started creating different SST profiles for each aircraft, but thought this would be a pain and reverted to using one profile generic enough for all of them.