Maybe a slight English issue here, not sure if I understand. The Archduchy of Austria and the Kingdom of Bohemia were part of the Holy Roman Empire. The Kingdom of Hungary, Croatia, Galicia-Lodomeria and all the other sundry possessions were not part of the Holy Roman Empire. They were a collection of feudal possessions some of which were inside the HRE and some not which happened to be held by the same person. I'll check this just to make sure but, it was impossible to apply Holy Roman law in Hungary, which had its own legal system. It would be like deciding to use French law in a British court.

Perhaps a better example of overlapping political jurisdictions would be the Duchy of Aquitane during the Angevin Empire. Technically, the king of England was vassal to the King of France, as Duke of Aquitane, while being independent as King of England. This caused the English real trouble as the Gascons would, if they disliked a particular policy, go and appeal to the feudal overlord, King of France, who would grant their wish just to make trouble for the English.

This was pretty common under the feudal systems of Europe. The most absurd examples are probably Frederick I of Prussia and Augustus II of Poland. Augustus II was initially the Elector of Saxony before being elected to be King of Poland. Frederick I was initially the Elector of Brandenburg, who just so happened to have territory in Prussia, before proclaiming himself King in Prussia.

These two men were contemporaries. This meant that, within the scope of the Holy Roman Empire, they were both subject to Emperor Joseph I. As Electors they were peers. Outside of the Holy Roman Empire, Frederick I was subject to Augustus II.

They must've had a very... interesting relationship.