Well, I won't be much help to you there I don't think.
Way back when, I found a website that had thousands upon thousands of c64 roms, and I wrote a spider to crawl the site and scrape them all. Thing is, I ended up with full filenames. I think I'd have rathered 8 char names, but I got what I got, and hey it works for me.
So... long story short, I just let mamewah do a rom_folder list, and I get like 3400 roms, all named very nicely.
That being said, your post did remind me of something. I can't get my mame roms to list properly in mamewah 1.62 using rom_folder_vs_listxml. It works great in 1.61, but for some reason the identical mame folder gives me nothing in 1.62; I think I remember somewhere along the line the parameter for mame changed, so maybe 1.62 is using some parameter not supported by my (very old) mame version. Who knows. I copied the 1.61 mame.lst file to 1.62, and it worked. If you were able to list c64 roms properly under mamewah 1.61, perhaps a similar trick would work for you?
Lotsa luck. I'm off to play paradroids.

Chemame