I think you're right...contractually speaking, anyways. Beckett knows his payday will come and he's still young so he's got one definite, probably two big deals in his future.
On the other side of that, if I were Beckett...I'd consider it somewhat of a slap in the face if I'm the ace of the team and carry the team on my back through the postseason, then they go out and get a new guy and I'm dropped down to a #2. For that reason, I keep Beckett the #1 and make Santana #2. Beckett's ego, to me, is the only thing that can be damaged this whole thing, and I think that that can be avoided if you go Beck #1, Santana #2.