Usually I'm on the "you're using it wrong" side but not this time.
Mostly from my experiences of fighting atlases, it's almost a joke at times.
When I see other assaults, I'm concerned and run for cover before I fight.
When I see an atlas I laugh and PPC snipe its head in a few volleys.
Now the Atlas is tough as nails otherwise and I would love to use it more, but I generally avoid using it and use the other Assaults.
Eventually I feel it needs to have the skull hitbox where the head itself goes to CT damage and only the eye/immediate face area, is head.
That would be an insta fix, you don't even have to change the model if you don't want to.