Well, it is Mame, and Mame is configurable, so it doesn't really matter.
I rock 3 1 2 4 but have to change it in most 3 or 4p games anyway. For instance, NBA jam is set as 1234 to match up to your on screen players. Turtles is set the same way to have the proper order at the top to match the coins.
That's the beauty of it, you can have it any way you like. 3124 will at least ensure every 2p game is set up right without any hassle.