Earlier quoted context omitted.
The concern is not about privacy, but about forced treatment against your will. That's a big deal, and most countries have strict law in place to stop it happening in most situations. There are some exceptions for people who are unable to make that choice, but this is limited to people who are not conscious, or who have severe learning disability, or who are currently severely mentally ill.
How exactly did we go from a scientific paper waivering requirements to use patient data, to forced treatment? I’m lost.
Because bronchoalveolar lavage, one of many procedures used here, is an invasive medical procedure that has no purpose other than to obtain information for diagnosis or scientific research. A small endescope is passed down the trachea, and part of the lung tissue irrigated with fluid, and the fluid (now containing cellular detritis) analysed. It is intensely uncomfortable if performed without sedataion and bronchoscopy is typically performed under heavy sedataion as a result. All of these facts carry risk -- risks which, under international law, the patient has to consent to.