For example, when Charles V was in charge, why wasn't Spain incorporated into the Empire, or the Polish lands of Prussia pre-dissolution, or also how Austria owned Hungary, yet Hungary itself was not in the Empire.
You're confusing statehood with personal/dynastic union; the Holy Roman Empire was a confederation of states, not of dynasties. The Emperor couldn't demand the allegiance of principalities that weren't a part of the empire, even if they shared a monarch with one that was. With regard to Spain, you couldn't have an official union of the two realms, because officially, the Holy Roman Empire had no ruling dynasty, since the seven electors could choose who they wanted.
At his ascension in 1506, Charles V held many titles, among which:
Soon, he added:
Later on he added: King of Romans, Archduke of Austria, Holy Roman Emperor.
Each one of these titles, and corresponding fiefs, had its own rules on the rights and responsibilities of the title holder, including rules of succession. So it was simply not feasible to simply add lands into the Holy Roman Emperor, which itself had rules on membership.
Austria did NOT own Hungary, rather the Archdukes of Austria gained control of Hungary and was able to keep it under their control.
You may learn more by reading Why Charles V never annexed all his possessions into one entity, further on his inheritance.
Even to say "... Charles V was in charge ... " is a gross over-simplification of how things were when he was ruler of those territories.