I'm not sure I understand the benefit of the "super max" NOT being counted toward the salary cap. In the scenario that the super max isn't counted, big market teams have a ridiculous advantage. The Knicks, of example, could offer George Steinbrenner type contracts to attract the best player on the planet. $100M a year may attract Lebron. Small market teams will still be limited by their capacity for income -- thus, probably could only compete with current "max" offers.
If Super-max counts toward the cap, big market teams would no longer have an advantage over small market teams for the top players, AND GMs would need to manage the cap -- keeping somewhat of a lid on what they'd offer for the Super Max. If a large number is taken up by the Super Max, the gathering of a super team will require 2nd tier players to take less $$ to play with the top tier guy (could happen, but chances decrease especially since all 30 teams can offer a super max slot). Good drafting, development of younger supporting players, and quality coaching will be big difference makers in the league.