I can echo your concerns because I ran into it with Spelunky recently - they seem to only support Xbox360 controllers as their "controller" settings. I solved it by using Joy2Key to map keys to my controller (a very solid Logitech one!) and had no problems.

However, most people probably wouldn't want to jump through those kind of hoops (downloading a third party app + mapping the keys to the right keyboard keys) so I'd love if Steam had some sort of unified controller support, but I also feel like that's asking for a lot.