I beg to differ.
1) The Mets Harvard GM should have been protesting this months ago when Pittsburgh was awarded the #9 pick since they didn't sign their #8 pick from last year due to Scott Boras' expectations that Mark Appel would be the #1 pick with a $7.2 million slot bonus vs. the Pitt. offer of $3.8 million which was over slot for the # 8 pick. The Met GM should have protested this immediately when the Mets were bumped to #11 from #10.
2) Now Scott Boras is having a hard time getting a BJ Upton deal for Bourn because it appears that only Seattle is negotiating. The Rangers are probably monitoring. Frankly, Bourn is not worthy of BJ Upton $ since he lacks power which Upton has along with a higher ceiling. So Boras is suggesting that the Mets protest the #11 unprotected slot so as to entice the Mets to get into the bidding.
The reason for the new CBA rules with regards to both the hard slotting of draft choices in the 1st ten rounds and the protecting of only the 1st ten draft choices is to keep the FA contracts lower & to prevent Scott Boras from manipulating the markets.
If the Mets get this exemption before they were to outbid Seattle or Texas, then Seattle or Texas will be forced to overpay for Bourn by then outbidding the Mets. In this scenario the only beneficiaries would be that Bourn would have an inflated contract value & Boras would be overcompensated as a result.