Yeah, I think it's just a preference. Me - I'm a neat freak so I find I'm washing saddle pads a lot, hence the baby pads, which definitely would look funny under a fitted pad, as they are square. I have fleece lined girths and I always am careful how often I wash them because they are more sensitive to that kind of thing. So that's why I go with the square ones (and because I have a CC jumping and a dressage saddle that would be tough to fit either of them perfectly).

Either way, there's no physical reason why either would be better. As long as the pad stays put and provides sufficient padding for the horse's back, you're good!