That's an interesting inrerpretation but I doubt it would stand the tests of the courts if anyone went through the hassle of pressing to test it. Can a CBA ratified by the majority force you into a religion? Can it permit racial discrimination? Just because you work under a CBA doesn't mean that CBA superceedes federal/state/etc law.

If a pilot stuck to his/her principles and HIPPA rights and refused to waive them, the FAR's/IMSAFE requirements would easily be more than enough to steamroll any company bullying in the long run, even if they decided to go nuclear and take pilots hostage over it for the short term. What would be even more interesting than that would be for a pilot to actually waive their HIPPA rights, allow a medical doctor (particularly a "company doctor" but any doctor really) and have that doctor write a "ops check normal, could not duplicate" letter, then have the pilot get in trouble over it. The legal and financial remedies available against the company and that doctor would be massive, and fully backed by the FAR's.

The only thing more flagrant than a doctor putting his/her name to something saying a pilot absolutely did not have a stomach ache/feel nautious/have ultra low viscosity emmissions/etc would be for an employer to financially harm said pilot because of a worthless opinion letter like it in the first place. A doctor can say you are sick, but they can't say you're not and they really can't say you weren't sick a few days ago. Some pilot is going to get very rich off of that kind of pilot pushing safety infringement eventually, or at the very least get a nice fully paid vacation.