During that tour, we learned that pretty much every stereotype Americans have for Germans (lederhosen, yodeling, beer and brats, etc.) are actually Bavarian culture, not German.

So for lederhosen, it's mostly true, although they're traditional in Austria too. Yodeling is Alpine culture and not specifically Bavarian, meaning it exists in Bavaria, in Austria and Switzerland. For beer, only weissbier is truly Bavarian; e.g. pilsener originated from Czechia, lager originated from Austria [til!]. And although there are Bavarian bratwurst variants, bratwursts are not specifically Bavarian. However, veal sausage (weisswurst) is exclusively Bavarian.

And Germans are actually quite offended at the confusion we have between their culture and Bavarian culture.

That is true. I think to some degree this confusion comes from the fact that so many Americans were stationed in Bavaria after WWII, so they only got to experience this part of German culture.

[...] when the war was over, they not only had to rebuild from scratch, but also had to contribute to rebuilding the rest of Germany, as well as paying for war damages for Europe and all Allied nations, etc. Their wealth was pretty much depleted and their hope of being an independent nation was gone.

I am not particularly versed in Bavarian history, but note that some Bavarians have developed a bit of a fetish portraying themselves as victims of injust decisions from on high. I would take that info with a grain of salt.