Hmm.. It doesn't have anything to do with MAME vs. Console ROMs, if I understand your question correctly.
ListGen, ListGen.NET and MAMEWAH Config can all sort your ROMs however you want, but MAMEWAH will re-sort them alphapetically on the fly. Minwah has stated this is intentional behavior, and he'll consider adding this as an option if/when he updates MAMEWAH with a new game list format.
Basically, this is a limitation/feature of MAMEWAH and can't be changed

-Steve
P.S. As for the console catver, I started a project for that (
http://www.bluecamel.org/software/catver/) but I didn't work too much on announcing it. The summer's here and it's hard to stay focused on this "indoorsie" stuff

). It's very much an open project and if you want to help out, I have the infrastructiure to take submittions all set up at
http://www.bluecamel.org/software/catver/ . Feel free to check it out, categorise some games or check up on the latest progress. It's a needed catalog that's currently unavailable, and I'm committed to providing it. Just as soon as I can

Oh, send me a DAT file for platforms that are not already listed and I'll put them up there for everyone to take a gander at.