Agreed. Since corporations and other legal entities are creations of the state, the state has the right to regulate how those entities interact with each other and with people. But only up to a point.
The state (or Federal government) cannot regulate a person's thoughts. Therefore, the state cannot regulate the creativity involved in the design of a particular agreement (thoughts such as who is our target audience; what are we willing to give as consideration in return for what we get from the signatories to the contract, etc.) In the design phase, all kinds of information are collected and considered. The state cannot regulate the design of an agreement. But it can and does regulate the implementation of that agreement (and any subsequent alerations of the agreement).
The article you linked to above concerned mainly the design phase of an agreement, not the implementation phase. Folks are free to educate themselves in whatever manner they see fit in the creative design phase of an agreement, including a Business Associates Agreement. But, as you've pointed out, folks are not free to implement such an agreement in whatever manner they see fit. The agreement must comply with state (and maybe Federal) laws- so it needs to be vetted by someone authorized by the state to vet the agreement. If for no other reason than for your own peace of mind that the agreement actually does cover your ass in the way the law requires.
