Just because management and labor agree to something in a CBA doesn't mean it is 100% immune from being overturned by a court of law. Don't get me wrong, overturning a clause in a CBA is a longshot.... but it does, on occasion, happen.
This isn't exactly your typical management-labor situation here. In this case, "management" is a group of 32 businesses who claim to be completely separate businesses when it suits them and then will turn around and claim to be 32 equal partners when it suits them.
There's the Union which literally tells every player to negotiate their own deal. This is unlike every other Union where everyone makes the same amount of money (based on seniority, time in position, etc).
Then there are the players entering the draft. They're not in the Union yet, but are still constrained by the CBA, which makes little sense. What makes even less sense, especially from a legal standpoint, is that there is no one in the Union who represents their interests. Quite the contrary, in fact. Every time a new CBA comes up, the current crop of players are all too eager to throw the next generation under the bus because no one can stop them.
IMHO, and after staying at a Holiday Inn Express last night, I believe if a lawyer ever tried to argue in court to overturn the draft, that's the tact they should take. The draftees should not be constrained by a CBA where not only were they were not represented in the negotiations, but the people doing the negotiating actively gained by taking away from them.