The only reason I know of for people to install the rolls with the flap towards the mounting surface is to prevent animals from pulling on it and unrolling it.
My arguments against mounting it that way that are:
1) my cat doesn't do that. She seems completely uninterested in the things in the bathroom (unless I'm in the shower) (and she's not able to get to the other bathroom)
2) it's easier to know how many squares you're pulling off (unless you're a neandertal who only buys the commercial grade stuff that doesn't have perforations)
3) you can make the little decorative triangles with the end of it so it looks nice