The skull doesn't simply indicate which enemy is the "boss," does it?
I have seen a lot of enemy groups and usually there's no skull at all on any of the enemies. I even recall fighting enemy groups in which a really radioactive/green Radroach or Feral Ghoul did not have a skull, but some other enemy did.
Best Answer
From this Reddit post:
This post seems to confirm this as well:
Also, from this post, it looks like all bosses will have a skull by their name (but from the previous posts, not all skull-ed enemies are bosses):
So, it looks like enemies with skulls by their names are not necessarily bosses, but are definitely harder than the average version of the same enemy.