I really find it hard to believe that Valve would agree to providing all of its services without getting a cut of each purchase, no matter how you purchase it. And it would be too much like StarDock stealing from Valve, which I find even more unbelievable.
I read into that a while ago and here is how I think it worked ( and presumably still works ).
Steam have a set of tools that they sell to Game developpers. This is what makes a game ''Steamworks''. It facilitates integration into steam and add features such as multiplayer communication inside the game, the all fabled accomplishments, DRM for piracy prevention and other things.
Devs do have to pay for that mind you, I think it is a one time fee but I am not sure, It might be a renewable contract and mayne also they have a little cut on the sales but I doubt it.
In any case, part of the SteamWorks package is that the game now requires Steam, hence each time the game is sold, a steam key is generated and the game can be activated on Steam. If steam insisted that all steamworks game be exclusively sold on Steam, not only would that have been evil, but it simply would never have worked.
Suppose Steam only charge a one time fee to Devs when they buy their Steamwork package. They still have to provide servers and bandwidth services that may cost them in the long run more than they were initially paid for, but then that generates traffic on Steam, and incidentally more sales in the Steam Store. The system does make sense and is mutually beneficial for both Steam and The devs.