Complexity has different meanings. People don't generally go and assign objective metrics of complexity to proofs, besides how long it is.
You could try to draw the stack of abstractions necessary to understand the proof and see how high it stacks, and you could try to call that fundamental complexity, but I don't think many people would be happy with that.
So yes, it's a difficulty in human understanding. What else could it be?
It's very common to track how many different axioms are needed for some result, and consider results with lower requirements to be more fundamental. "Less complex", probably not so much, but the issue is something that a number of people care about.
You could try to draw the stack of abstractions necessary to understand the proof and see how high it stacks, and you could try to call that fundamental complexity, but I don't think many people would be happy with that.
So yes, it's a difficulty in human understanding. What else could it be?