i generally use touch align then infer center/axis for cylindrical mating.
The center mating option you're referring to can be used for centralising cylindrical geometry in a square hole when there is clearance between the faces or a square insert in a square pocket that also has clearance between the faces.
watch the below link..you will get understand,,
If one oblong hole and another is just simple hole,so ,if we want to contrained in such sitituation we are use center command