Honestly, I think all of this talk about numbers is pointless. The way the salary cap works, in 90% of the situations, there is not a big difference between a $9 million a year contract, and a $12 million a year contract. Most of the time, you are still going to be over the cap.
Teams are not killed by overpaying elite, building-block players by a few million a year. Teams are killed by signing flawed, non-elite players to elite level contracts (I would consider an elite level contract, pretty much anything in the $10+ million a year range).
I feel strongly that if the C's felt confident that Rondo was an elite level player, this would have gotten done a month ago. However, I think they are still not convinced, and have decided that it is worth the risk to pay him a little more next season, in order to be a little more sure they are not screwing the team over by putting their future in the hands of the wrong guy.
Ultimately, it really is not going to make a huge difference in 3 years, if Rondo is making $11 million, or $13 million. Because if they sign him for a "bargain" at 5 years, $50 million, and he turns out to be Kirk Hinrich or TJ Ford, once the Big 3 are gone, then the team is pretty screwed. But if they wait a year, and sign him for 5 years, $65 million, and he turns out to be close to the Chris Paul/Deron Williams category, they are not going to care that they paid a few million extra, because they are going to have the production to match the money.