The difference are that the Czech already had a rather developed national identity even before their national awakening, while the Slovenians hadn’t. They had been treated like any other Austrians for a millennium, while the Czech thanks to the political structure of Bohemia had been treated different. The Poles are also a bad comparison as a strong Polish identity already existed
This doesn't really matter as Slovenians were already developing an identity as well and the Czechs weren't really that "developed" as they also experienced similar things to many other nationalities during the late18th and 19th century:
https://en.wikipedia.org/wiki/Czech_National_Revival
I'm not sure how much the different political structure matters, if anything Bohemia was ruled pretty strictly during the 17 and 18th century.
It’s core part of the Austria, because it have been in union with the rest of Austria for so long. You could just as well ask why Styria or Carinthia was core parts of Austria.
Well ruled 2 centuries more than Bohemia, but I don't think that's really what makes something a core territory.
Also yes, I would say both Styria and Carinthia are not core territories of the Austrian state, even if just taking Cislethania in consideration, the core of the Austrian states was "always" the Danube valley, Pannoia, Czechia and Slovakia.
Strange, why does Prussia get to keep its land outside of the German Confederation but not Austria?
Anyways as others have stated Bohemia probably gets a fair amount of autonomy.
The Slovene national awakening is already underway so I don't see them being assimilated. However, like Lusatia, I don't see it gaining any formal autonomy despite their distinct and geographically contiguous culture. Unless of course this Germany's constitution had some goofy provision that would make that desirable for cynical reasons (like if there was some sort of representative body where each member kingdom got one vote, in which case a Slovene kingdom would increase the Habsburg vote by 50%).
Prussian territory had a large portion of Germans and a relatively small amount of minorities, a relevant portion of which was still Protestant, in this case Austria could probably take Ödenburg/Sopron and Preßburg/Bratislava and push the border eastwards but even the territory inside the Gemran confederation have a lot of non-Germans. The 2 situations are not comparable for this reason.
But why would Bohemia get autonomy over Slovenians? There are substantial amounts of Germans in the region(1/3 of the population), the religion is catholic and the area is a core industrial and economical regions surrounded by German land.