The problem was not Joseph´s skill as a negotioator but the opposition of Prussia under Frederick II. He created the so called Fürstenbund to oppose this trade even started a war. If you handwave all of this the biggest consequence would depend how the recompensation (Reichsdeputationshauptschluss) is handled (except they somehow win the First Coalition War).
I see two ways it could go either Austria is forced to cough up former Bavaria or they get most of central (Bm. Würzburg, Bamberg, Fulda and Ebm. Mainz) or northern clerical lands (Bm Osnabrück, Münster, Paderborn and Ebm. Köln). In the first scenario the timeline would change back to his original state with some resentment in Bavaria agianst the Wittelsbachs for trading them to Austria (they did not want that). I doubt that german unification would change. Maybe Bavaria would change into the Prussian camp in the Austro-Prussian-War.
The second scenario would alienate Prussia , which gets less than promised out of its peace deal. This could lead to Prussia joining the Third Coalition or not (FW III was kind of an indecisive man). This timeline would be completely different.
The new territory is in the north of/central germany therefore they don´t have to choose a side in the Third Coalition War. They could join Prussia in its suicide attack.
It would lead to major changes in the future. Austria could unite germany in a "großdeutsche" (big german) solution or even a "großösterreichische" (big austrian) with a bigger foot in germany through Bavaria.
One thing I can say for 100% is that this land would not join the Netherlands. The Wittelsbachs have no intention to give lands for nothing and the Netherlands had nothing to give.