I think XPlane is fully Cross Platform. I actually built a brand new PC for Assetto Corsa and DOTA2. The ability to run the other games that my MBP struggled with is just a bonus.

If it can stream Gamepad controls, can it stream mouse/keyboard/wheel as well?

It streams KB+Mouse (obviously). Not sure about wheel. It's unlikely that it will simply becuase there's a lot more state and variety with wheels (plus FFB). The best "workaround" I could think of is to plug wheel directly into your streamed PC, and then use the destination PC as a monitor but that's assuming that your boxes are adjacent (and in that case, why not just use the other box!).

Would the only problem with dualbooting windows on the Steam Machine be the lack of drivers? Unless they specificly block the software, I don't see any reason it can't be done.

No, It's all standard PC hardware, so Windows should run fine.