Let´s explain it to you. King A holds duchy of Hamster. This duchy, though, is considered to be part of kingdom B by its ruler, king B. King A, of course, doesn´t care. In his mind, Hamster is part of his realm. What this guy rightfully sees as stupid is that king A is not allowed to appoint bishops in duchy of Hamster, because king B considers Hamster to be part of his realm.
The problem for king A would be that, of course, not only king B still considered that duchy a part of his kingdom, but the other nobles in Hamster (and elsewhere) as well. Or, for example, the pope. So, even if he simply appointed a new bishop, what was he to do if the pope excommunicated that person as usuprator and his subjects followed suit with that excommunication, accepting the pope's new bishop instead? Waging war against the nobles in Hamster, who would probably be supported by King B who is only waiting for a chance to "free his loyal subjects from A tyranny"? Forcing him to accommodate his other nobles, who worry that he might try to ignore their privileges next? Not to mention that his struggle would bind his ressources, thus giving his enemies an opening?
Basically, it would be something only a strong king would pull off - and something he would have probably to repeat several times before his final say in that matters was finally accepted. That is what CK2 represents as de jure shift:
Other's accepting that A is now in full control of Hamster. Not that the king itself accepts it.
Don't get me wrong, the de jure system does need a serious rethink - even in 1066 in places it is borderline wrong/inaccurate.
If I understood it correctly, several of these errors were introduced for technical reasons - everything must be part of a
de jure empire, all duchies need to be part of a
de jure kingdom and a
de jure empire, all counties need to be part of a
de jure duchy, a
de jure kingdom and a
de jure empire. The earliest versions did not require that (they introduced new empires at some points), but several mechanics would break in the recent versions otherwise. At the moment, the de jure system is rather clunky, but probably the best they can come up with given the circumstances.