Why should Austria inherit Bohemia and Hungary? It was a vague thing until a day before it actually happened - Lajos II died young. There had been a royal marriage that triggered the PU. That's it.
As for Venice...it's simply that "Our Claims to Northern Italy" has to go. In 1492, France has cores on Milan, and there is an Italian Wars DHE. That's all that is needed - and what is better is that it doesn't touch Venice. As it should be.
but it was a thing that made austria what it has been... the habsburg family was origianlly a very, very small and not powerfull at all noble family from the north of swiss... it has built its greatness over 800 years of lucky (and very smart) marriages, all austrian power derives from royal marriages and inheriting... if u cut that off the game then austria shouldnt be big or powerfull at all, not more than a normal medium european power at least.. more like a less powerfull portugal with no trade richness and no navy or colonialism (except for the eventual emperor buffs ofcourse)
if, on the other hand, u like to see the usual french-austrian costant clash that happened in history, austria should be at least able to inherit bohemia under the same lucky conditions... but if u take that off it should be entirely possible for bohemia or even brandeburg to take over the empire crown, and without the empire title, the habsburg whas nothing more than a medium power