I'm more concerned about de jure ducal vassals of de jure empires. Being allowed to create a de jure kingdom is one thing, though some of the core kingdoms of certain empires (ERE & HRE) are problematic too; but a custom titular kingdom, as a vassal, IMHO should be something different.
Certainly de jure vassals, those IMHO should need the permission of their liege (de jure & de facto).
I'm totally fine with independent dukes, once powerful enough seek a royal crown. It's only vassalized dukes I'm concerned about.
I agree that the inner workings of both ERE and HRE should be revorked greatly, those two entities should simply not be acting just like another realm. But I dont think we will see that ever in CK2.