Honestly, I can see both sides of this argument.
Under is more pet-proof so they can spin it without you worrying about them emptying the roll, and it gives you the tool itself as hand resistance if you decide to tear a few pieces off, though only with an underhanded grip.
Over is much more visibly conducive to finding the last square in the case that it's fused to the roll somehow, and tearing off a square only requires bracing your middle finger down against the roll to tear a piece.
I guess the clearest way to decide is this:
Do you prefer to tear a square off the roll using the closer hand (Under), or the further hand (Over)?
These positions are best suited to actually getting toilet paper from the roll most comfortably from either position, otherwise you are making it less comfortable for no reason.