The executable is the same. Some people have found that the performance of the Rift is slightly worse when using SteamVR, though I don't believe I've tried it myself. I can't remember anyone mentioning any difference between the FD launcher and Oculus Home/App from a performance point of view.
...if someone were to force the game to use SteamVR over the native Oculus runtime - Not that I can see any actual reason as to why someone would do that really.
Previously either BigScreen or Virtual Desktop (I forget which one now) was only available via SteamVR but yeah that's the only reason I can think of (other than "I want to access all my games via Steam").