Usually, an entire contract is assigned to another team -- assignment is what is discussed in the CBA. So, if Crawford is traded, I don't see what rights the Red Sox have in his contract, and his new team should be free to negotiate any change in the contract, so long as that change is approved by the Commissioner's office pursuant to art IV of the CBA. (There is a limited exception for the ARod type situation where the MLBPA attempts to assert itself in the approval process, but that is pretty thin ice and we can imagine a situation - Crawford is offered $1,000,000 -- to make that inapplicable.)
I'm left still not sure what this accomplishes.
Even if your interpretation is correct, it gives enormous leverage to CC he basically gets to negotiate a whole new contract for whatever he can extract. It may not render it impossible for him to end up in New York, but surely adds some legal and financial hurdles.
It'll be interesting to see the repercussions of this innovation (assuming it is new). Will other contracts, even low-rent things like Albers or Martin, start to pop up with similar clauses.