From this Reddit post:
Mothers, Glowers, and Alphas- With the addition of quests came the need for bigger, badder monsters. These enemies are unique versions of our regular enemies, with a red skull near the right side of their health bar.
This post seems to confirm this as well:
In Wasteland locations, sometimes you will encounter enemies coloured Green or having a Skull on their health bar. The Green Ones usually cause high Radiation Damage while the ones with skulls tend to have more hitpoints than the regular enemies and may even call reinforcements.
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):
Q: Why are some enemies really strong?
A: It's probably a boss enemy. All bosses will have a skull next to their health bar to indicate this.
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.