From playing this game for a couple days now, i think its weird that superior foes seem to take way less damage than if i were 1/2 lvls higher.

Even quite early in the game this is the case with the brown bears. They end up killing you with just  a couple hits (which is totally fine, dealing more damage to "lower" enemies should work both ways, for player as for enemies)
But i dont think there should be a penalty for killing higher level enemies.

Imagine you get attacked from a bear in real life. Full armored dude with a knife would end up killing the bear (maybe) but if you get attacked and have nothing but  a knife each stab might end up dealing the same damage (if you know where to stick it :D) and given that were dealing with a pretty old beeing thats been on this realm for who knows how long- chances are they know what they are doing! They are just in a weak body.

I get it from a design point of view, it makes the game much harder if you dont follow the correct path, but i usually end up going for "no challenge" enemies of my level. Maybe just have it as an option.

The level difference doesn't affect the damage you deal or is dealt to you in any way. And you will get a small bonus exp for killing higher level enemies.

These enemies are stronger because some inherently have higher resistances to certain things. Like mummies might have no fire resist or even negative fire resist, whereas skeletons might have higher resistance to nature damage. Not saying this is the case, but its an example.  As you face harder enemies, they have higher resistances innately.  Also, definitely hold shift to look at their equipment.  That way you can see if they are wearing something "of the tempest" for extra electric resist etc.