Everyone is basically following PayPal's lead. To make price a compelling differentiator, you'd have to go to a place where it'd be very difficult to make money. 2.99% looks kinda lame. 3% is perceived as much higher. PayPal's choice was spot-on.
Here each processor is trying to achieve a market position relative to their competitors almost as an epsilon. They want to be seen as cheaper but no cheaper than necessary, and they want to retain simple terms. That drives them to tweak the 1st and 2nd order terms (constant + a scale factor).