I might be totally wrong or misinterpreting the results I am getting. I tested this and it seems that, at least on mine, it picks the rom in the same order as the list that comes up when right clicking a title. That is to say, if the list was ordered such: rom (europe).rom, rom (USA) (Beta).rom, rom (USA) rev 1.rom, rom (USA).rom it will select the first rom that matches that region preference in the list, which is ordered in alphabetical order, in this case the USA beta rom. If another rom was merged in the same set labeled something like rom (USA) (Arcade).rom, it would select this rom over the beta one.
That being said, maybe there is some config option I turned off and didn't realize or maybe I am misreading results. It's not some massive priority though, considering anything I was playing or planning to play can be switched over easily without having to remove the other file, I don't want to sound like I'm complaining.