Time crystals aren't the only thing that has properties that change in an orderly, predictable fashion. Plain old uranium has the same property. The answer to both is the same - put them on a very fast rocket and do a lap around the galaxy and see how well they agree with you on how much time has elapsed.
Is it not rather that time does not elapse everywhere at he same speed, simply put?
Based on this, of course, measuring it becomes difficult.
It's akin to measuring gravity. You can — for a specific point in space and time. (Time is even worse, since it is specific to a given _trajectory_ in space)
It's identical to measuring gravity. In relativity, acceleration and gravity are indistinguishable, and it's acceleration which breaks the paradoxical symmetry that gives the name to the twins paradox.
