LeCHVCK's points was that Germany would have an independence revolt at the drop of a hat, and it wouldn't be one easily placated
Hungary had an vested interest in staying together with Austria for much of the unions time (mainly the fact that if not, then the Ottomans would come visiting not intending to leave)...
And even so there was a lot of restiveness in Hungary.
The 1500s saw a prolonged three-way conflict between the Hapsburgs, the Zapolya Princes of Transylvania, and the Ottomans for Hungary. Transylvania remained quasi-independent through the 1600s.
And not long after the Hapsburgs drove the Turks out of Hungary in 1699, there was a Hungarian national rebellion against the Hapsburgs.
Hungary also a had a much stronger tradition of national unity. Until the Tiurkish conquest in 1526, Hungary was a single sovereign state. That Kingdom of Hungary, after some pushing and shoving, survived as Hapsburg Hungary, and then was reunited with the rest after 180 years.
That gave the Hapsburgs a leg up in ruling Hungary: after 1526, they acquired 1/3 of the old kingdom and a claim to the royal title; that claim was secured around 1570, with the demise of the Zapolyas. Then when the Turks were driven out, the Hapsburg title naturally inherited the rest.
Germany had been thoroughly fragmented for several centuries, and Napoleon could not claim the Imperial title that nominally headed the HRE. His house had not ruled part of Germany for several generations, nor led wars against an external enemy of Germany.
The only way he could make it stick, IMHO, would be to create a wholly separate German state, with nothing sliced off for France, run entirely by Germans loyal to him. This state would be a vehicle for German nationalism and liberalism against the reactionary princedoms, ecclesiastical states, Imperial city oligarchies, and foreign overlords - e.g. the British Hanoverians, Danish Oldenburgs, Prussian Hohenzollerns, Austrian Hapsburgs. (The Wettins and Wittelsbachs might be co-opted.)