Gustavus Adolphus dies in one of his wars with Poland (1626-1630), leaving the small Christina (which would 0-4 years old by the time) on the throne, no Swedish intervention means the war ends not much after Wallenstein defeats the Danes in 1629.
A preliminary peace treaty can be found there, ITTL it maybe even harsher since the Emperor wouldn't be trying to win support against the Swedes.
The HRE itself would still be fragmented compared to France, England and Sweden, but without the small states plotting against him, Ferdinand III and his successors would be better off, specially since now the Empire would have it's own army.
Over the long term, he and his heirs would probably be as eventually successful as the other European monarchies who were turning their medieval kingdoms into centralized states.
An Imperial victory would establish an effective government over all of Germany instead of its components becoming de facto independent states. Westphalia or Brandenburg would be no more independent than Brittany or Provence. However, Germany would still be behind France, Sweden, and Britain for quite some time as they were far further the process.
There would still be the case of some level of autonomy for the various domains, but the triumph of the Habsburgs would set the stage for further consolidation.
The problem is that Bavaria/the Wittelsbachs were pretty pro-independence (Max I of Bavaria and his descendants all the way to Max III, followed a Wittelsbach-first policy) even when they were married to Habsburg archduchesses. By smacking down the Protestant princes TOO much, you're essentially getting rid of the checks on the Wittelsbach power.
So, sooner or later, an emperor is going to have to make nice with the Lutherans/Calvinist princes to so that he can humble the Wittelsbachs. Except that Wittelsbachs have an ally in France, who'll supportany prince (30YW proved that just because you are Catholic doesn't mean you have to support the Catholics) who wants to stir trouble in the empire.
Note: simply using the Wittelsbachs as an example.
Yeah, the structures of power within the Reich are such that it's actually really hard to transform into a modern type state. Any disruptive forces are going to tend to fragment it into multiple independent states, not unite it behind the Habsburgs.
Personally, I'm much less interested in exploring turning the Reich into a unitary, Habsburg-ruled German nation-state than I am in exploring the weirdness of the Reich itself.
True, but France was even more decentralized before 1204, and the disruptive forces were even greater. Hell, the king personally held a smaller portion of the kingdom than the Habsburgs within the HRE, and foreign kings were more powerful inside France than the king himself, and easily held more than half of it.
All the structures in France would indicate that it would be hard to transform it into a centralized state.
And even when it tried to centralize under Philip II, it was met with tenacious resistance. In 1214, England, Flanders, Boulogne, and the Holy Roman Empire under Otto IV organized a coalition to crush France and preserve the liberties and independence of the great French vassals.
In my view, France in 1180 was even more decentralized than the HRE in the 18th century. You have foreign kings who are also vassals? Check (Champagne-Navarre and the Angevevins for France, Brandenburg-Prussia, Saxony-Poland and Hanover-Britain for the HRE). You had Kings defeated in war by vassals? Check (the King of France was repeatedly defeated by the Norman and Angevins during this period. The Habsburgs were defeated by Frederick II of Prussia.) The dynasty was legally elective but defacto hereditary? Check. You had foreign kings interfering with the kingdom? Check (France by the HRE and England, HRE by France).
In my opinion, all you need are a series of consecutive great emperors that would be on par with Philip II Augustus, Louis VIII, and Louis IX, to make the 18th century HRE as centralized as the France of Louis IX and Philip IV. And of course, lots of luck.