Regarding following examples...
When Napoleon heard about Wellington's retreat to Torres Vedras and his and the Portuguese's wastage of the land and resources, as well as the forced evacuation of the native population, he was very impressed. But when he was urged to do the same thing in Saxony in 1813, he refused as he believed it dishonorable to behave that way to an ally.
Therefore, I do believe that Napoleon did not waste and destroy his allies assets in Germany during the period. He did require supporting armies from the states of the Confederation, but he also pledged French troops to their defense. And that system worked in 1809 in defeating the unprovoked Austrian invasion of Bavaria and the subsequent defeat of the Austrians by the Army of Germany that was composed of at least one-third of Confederation troops.
Wurttemberg, Baden, and Hesse-Darmstadt were members of the Confederation as long as Bavaria was and lasted longer in 1813, especially Wurttenberg.