You are wrong on all points.
When Hofer assumed command of Tyrol, Franz was incapacitated by some upstart called Napoleon. He was no longer in Vienna.
The uprising in Tyrol had the full approval from Vienna. It was not a spontaneous rebellion.
At the time when Hofer assumed command of Tyrol, there was no government to rebel against.
Hofer was as legitimate, maybe even more so, than the usurper Napoleon who did overthrow and rebel against the then legitimate government.