I assume a POD in the 1520ies or 1530ies.
At this point, Baden, Würrtemberg and Bavaria are smaller than later in the 19. century or the two Bundesländer Baden-Würrtemberg and Bavaria today. Many smaller territories and free imperial cities are between them. Also todays northern Bavaria, the Region Franken is at this point not a part of the duchy of Bavaria. And the Palatinate (Kurpfalz) controls some parts of todays northern Baden-Würrtemberg. Therefore you would control not all territories in southern Germany, but just 2/3.
But if the House of Habsburg tries to conquer not only Württemberg (as in OTL) but also Bavaria and Baden, it would be plausible, that most of the "Reichsstände" (the principalities, duchies, bishoprics and imperial cities) would unite against the Habsburgs and cooperate with Phillip of Hesse, even if there are confessional disagreements. France would perhaps oppose this increase of the increasing power of the Habsburgs. The Swiss Confederacy would be frightened too (but is in the 1530ies in civil war).
It is possible, that the Austrians could maintain these possessions, and even try to create some connection to the Netherlands.
A victory of the Austrians would still mean, that many "Reichsstände" in Northern or Central Germany would oppose any centralization. And France and the Ottomans are still powerful opponents. Therefore Catholicism could regain Southern Germany, therefore separating the Reformation in Northern Germany and in Switzerland. This could perhaps change the Reformation in the Netherlands, or even mean, that the Netherlands remain Catholic. But the Institutions of the Holy Roman Empire wouldn't gain more functionality, because the confessional groups could still easily block each other.
Straßburg could be threatened from the Austrians. And Straßburg was a really important center for theological discussions in these decades. This could change the development of the Anabaptist movement.
And what about the Anglican refugees under Marry Tudor ("bloody marry")? They would perhaps flee towards other countries, which would change Anglicanism significantly after her reign.
I don't know enough about the Huguenots and the Reformed Church in France to give some estimates about possible changes, but I would suggest, that this would change their situation to.
But a victory of the Austrians could change the religious landscape of Europe, and later of the American Colonies.
But in OTL Phillip of Hesse managed to regain Würrtemberg for the Lutherans. Therefore a defeat of the Austrians is also possible (or a little bit more possible than a victory of the Austrians). Such a large defeat would weaken their position inside the empire and strengthen the Reformation. The effects on the constant struggles with the Ottomans could become interesting.
It is also possible that Phillip of Hesse succeeds in this case in bringing the Lutheran Reformation into the Bishopric of Münster (where he failed terribly OTL), and therefore strengthen the Reformation in the Rhineland.
If the Reformation succeeds then also in Trier or Cologne (I don't know the strength of a possible reformation in this area, and can't therefore estimate a probability for this scenario), this could create serious problems for the Empire, because there is now with Brandenburg, Sachsen, Cologne and Trier a Lutheran Majority among the "Kurfürsten" (Electors), after that further conflicts between the "Reichsstände" and the Austrians are only a matter of time.
I apologize for any mistakes in Grammar or Language, English isn't my first language.