In 1805, before the Confederation of the Rhine was founded, Bavaria, Wurttemberg, Baden, and Hesse-Darmstadt chose France as an ally instead of Austria and/or Prussia, because there was a much better chance with France of staying independent. France wasn't trying to ingest them; Prussia and Austria were...

A very telling indicator of which 'side' these small nation-states preferred was in 1809 when Austria invaded Belgium (without a declaration of war by the way) and the Archduke Charles issued a proclamation 'to break his German brothers' chains.' The proclamation, with a few minor exceptions, fell flat and the Confederation enthusiastically responded to its own defense and contributed mightily to the new Army of Germany that Napoleon organized to fight against the Austrians.

K