Let’s take the cases you cited one by one...
RE: If they are holed up in a cave in Yemen plotting against the U.S. then why not?
I was for it. I consider that an act of war and treachery. In which case, blowing up an American Jihadist like Al Awlaki is justified ( and we did ).
RE: If they’re barracaded in a compound in Pennsylvania ready to give the order that will set a terrorist bombing into action then why not?
Now that’s a little different. If we knew he was in a compound in Pennsylvania, we could always surround the compound and wait him out.
If we knew he was going to give an order to set a terrorist bombing into action, it would be better to capture him to find out where the action or future actions are going to take place.
It would be better to capture him than to kill him.
Wouldn't that be true in both cases?