One thing that immediately comes to mind is CPU’s branch prediction algorithm.
In case of > comparison, in sorted array the branching behavior is very consistent: first, the if condition is consistently false, then it is consistently true. This aligns very well with even the simplest branch prediction.
In unsorted array the result of > condition is essentially random, thus thwarting any branch prediction.
This is what makes the sorted version faster.
In case of == comparison, most of the time the condition is false and only very rarely it is true. This works well with branch prediction regardless of whether the array is sorted or not. The timings are essentially the same.