Can a Commander call my PA and get my medical records?

I can't speak to the actual interaction you had with your Company Commander, but it is routine for providers to communicate medical non-deployable updates to the chain of command. There are times where providers have to communicate with command teams to ensure the soldier is not being placed at higher risk.

Are you nondeployable?. Nondeployable soldier status is reviewed ad nauseam in conjunction with USR. In 2016 Senior Commanders (Division Commanders) were getting dragged through broken glass over deployability numbers and ensuring soldiers are not adrift in the process. Part of this is whether it is something that can be resolved in 6 months or less or it is a longer term issue where a med board may be required. In turn Brigade commanders got dragged through broken glass, the. Battalion Commanders, then Company Commanders. I can't imagine it got any easier since then. If 10% of the Army is non deployable, that's over a Division that can't deploy. Frequent profiles also draw attention, which is now traceable in MEDPROS. Temporary and Long Term ("permanent profiles" now have to be validated every 5 years).

Your commander may only have what you release to him and the information your PA deems relevant. Even then, the PA can't release your records without your consent. Accessing your medical records without your consent is a violation of HIPAA, which is a federal law.

I feel like there is a lot left out of this story.