I never cared and neither does my butt! lol Recently, it's been brought to my attention that in business places, over is the way it's done. My toilet paper holder is independent...stands on the floor. :)
I think that "over" is better because the coefficient of friction is slightly lower...not that it's a huge difference, but why make it any more difficult?
In the old days, toilet paper actually had patterns, e.g. flowers, and the only way you could see the pattern was to mount it so the paper flowed OVER.
Sometimes when we travel we splurge and stay in an upscale hotel. And the maids always make a fancy fold on the tp roll when they clean our room. That's only possible if the roll is "over".