I don't think it makes a difference in terms of having to sign him now. The Sox are still not getting any benefit from all of the risk they are taking.
Not that I would do this deal either, but if Mookie is expected to make $35 mil AAV as a free agent, then the contract offer now should be in the neighborhood of $30 mil. Mookie leaves a little money on the table for his free agent years, but he gets more money for his remaining arb years, not to mention the long term security. And the Sox get a bit of a discount for taking on the risk.
If the Sox are going to pay him market value anyway, then just wait until he hits free agency to offer a contract. See how things play out over the next two years.