Your ruler is Emperor of the Holy Roman Empire but only Archduke of Austria, it's not that odd. Especially given that the HRE title can be passed on to the ruler of an entirely different TAG.
And in EU not all entities start equal, the detailed historical start is one of its selling points. Neither Bohemia, Baden or Austria are the same but they follow the same general rules. Bohemia starts as a kingdom and an elector, other tags need to get electorship first and can then become a kingdom (which is a pretty light rule compared to history).
No country can be both a subject state of the Holy Roman Empire and an empire of its own, if you're big enough you can leave and create your own empire instead.