From my experience in Germany reading many LBA manuals and ANO's as far as i'm aware, when the doors are closed the law of the land goes down to registration of the aircraft but that's is only for the occupants of that said aircraft (effectively a seal), once doors are open you must adhere to the law of the state to which you have landed.
Example
A/C is on ground in ALC
D- registered, German law will apply when doors are closed & A/C is sealed
when doors are open Spanish laws are then enforced.
as for the situation you encountered if it is not the state law then you have no legal right to exercise, however the commander does have overall say who can be onboard the aircraft, I think what was lacking was a little respect, with current events as they are the person could have simply put a mask on during their time onboard.