From my point of view, the causes of the uprise are manifold, under them political, religious, economical and military (introduction of the conscription) rationals:

I guess Napoleon considered in the beginning the Tyrolean uprise a "small domestic" Bavarian problem. Hence he sent in the first offensive (May): 2 Bavarian Divisions, less than 15.000 men (Deroy had in the two Battles of Berg Isel, 25th and 29th May, only 4.000 men in his division, cf. Maretich).

Later Napoleon´s view changed obviously. He detached:
+ in the second offensive (July/August, after the armistice of Znaim): 2 Bav. Divisions, Division (of German princes) Rouyer, corps Arco, Oberndorff, Beaumont etc.: ca. 25.000 men (my rough estimate) + 15.000 from the south (Italian-French troops under Castella and Peyri), in total ca. 40-50.000 men
+ in the third offensive (November, after the peace of Schönbrunn): 3 Bav. Divisions plus the Italian-French Divisions Rusca, Severoli, Barbou, Broussier, Durutte; in total 8 Divisions, more than >50.000 men

I will go more into the details in my talk in Vienna (about the Bavarian troops in Tyrol) next year.

Best regards, Thomas