Are not the kdm of Bohemia and AD of Austria intrinsically linked at this point unless separated by treaty they come as a set by this point in time.
If Charles captures Vienna he is not likely to give up either title. If he is Elected Emporer he will also include that title. It is not whether this is an Austrian or Bavarian Empire. It would be a Wittelsbach Empire in the same manner that it was a Habsburg Empire. There was no Empire of Austria until the Napoleonic Wars. The kdm of Hungary was held separately and distinct from the Hapsburg holdings in the HRE. It was personal union.
Charles would be thus HRE first, King of Bohemia ( as it is within the HRE), then Dukes of Bavaria and Austria ( or GD or AD if you like ) as perhaps Bavaria would be combined directly with Austria (Would they move the capital to Linz perhaps).
On another point, MT did not trade away Silesia for the A. Neth. it was lost militarily to Frederick and could only have been regained by prolonging the War and there is no certainty that that end would be obtained.
She retained the A.Neth at the insistence of the Dutch and British ( who were loath to have it go to France. Her own preference would have been to retain Silesia and let the French ( or someone else for that matter i suppose) have the A. Neth. Frederick would of course not give it up as that was the whole point in the first place as far as he was concerned. I can't remember what the French got out of this for withdrawing, but I think it was return of of their overseas possessions that had been taken by the Brits.
So the question comes, if Vienna falls will the French still be in a position to take the A.Neth or will hostilities end before they have progressed that far.
The Br. and Dutch will for the same reason's as OTL still be loath to have the French take it So it is likely to go to MT as a consolation if the Hungarian Nobility do not in the end rally to her cause. Though in truth, while they do not initially rally there is no reason they should not later on, as it avoids infighting among their own for the priviledge of occupying that seat.
If MT does not get A. Neth at the insistence of the Du/Br as a buffer to the French (and lets face it her husband is Duke of Lorraine right). Then the Br/Du will probably prefer it go to one of them ( or anyone else for that matter, their has got to be cadet branch of some ruling house somewhere that would be acceptable) whether they can make it stick is another matter. Personally I think the logical thing is for it to go to her.
As to Hungary, Salic law doesn't strictly apply does it There has been a suggestion that it was hereditary in the Hapsburg male line. Even then, wouldnt. Agnatic succession still apply, In which case MT is still the nearest Female to the last reigning male monarch or the realm. So even if they did not at first rally they might elect her and her heirs subsequent to this. Having Frederick take Silesia is probably going to make most loath to having the Hohenzollerns gain Hungary as well even in a Cadet line ( of course if they were a Catholic branch, that would change things significantly...does the Hohenzollern-Sigmaringen line exist at this point?) From the Hungarian point of view, there primary opponents would still be the Ottomans so they would want someone with ties that would be able to help them on that front. They would also need to be Catholic or convert I would suspect (a cadet Bourbon branch, because of their Ottoman ties would not be good bet. A Spanish or Italian line are probably the best bet, mind you that would bring back a Bourbon again right)