While a stop may be legal, a conviction is not. An arrest (citation) may not be as well, depending on the circumstances. A mistake of law should not be able to give probable cause for arrest. A mistake of fact, yes.
A cop can pull over a person he thinks violates the tint law. He has a reasonable suspicion to believe the law is broken when he sees the darker window.
He can issue a citation (arrest) to the person if he reasonably believes the window was tinted too darkly. Even if it was not. This is a mistake of fact which the arrest will be legal as there is probable cause. It would be up to the driver to defend himself in court. (Actually, for the state to prove the elements of the crime.)
He should not be able to issue a citation if the tint were legal based on a medical exception in another state. (If the question was just if it was too tinted and was legal in one state and not another, the previous paragraph would apply.) Because the tint would not be illegal and to think it was would be a mistake of law and not of fact. This is the same as the front license plate requirement in CA and not in some other states.
Zinger is right as far as a key question is where the person is a resident of and the related registration requirements of the vehicle.
(You can read a lot of cases on the internet if you look. Amazing what you can discover.)