What's the best way to detect whether your hero unit (i.e. you have only 1 of them) is in a bunker?
None.
Center a 1x1 pixel location on them, check to see if a bunker is there(obviously it isn't an air unit, or it couldn't go in the bunker.
None.
We can't explain the universe, just describe it; and we don't know whether our theories are true, we just know they're not wrong. >Harald Lesch
When the player brings at most 0 <hero unit> and at least 1 <hero unit> to anywhere then he's in a bunker.