Hi matrigs,
Well, it doesn't exactly work like that. The existing roms are not considered. The ini path is provided just in cases where you need to create inis for each game, not the case of GM.
donpachi is a vertical game, so unless you set the right monitor orientation option in vmmaker.ini, its resolution will be calculated as rotated so you won't find a 320x240@57.55 Hz a such. Set this option as 'rotate' to calculate both horizontal and vertical resolutions without any rotation.
But unless you're using the 'static' mode list method, you won't get the 57.55 Hz refresh, because everything is normalized to 60 Hz in order to reduce the list as much as possible, and GM recalculates the right refresh later.
If you still don't get the intended resolution, you can add the rom name the MameMain.txt file: the names defined there are considered as high priority so they shouldn't be dropped in the first place.
Finally, the list is not narrowed randomly at all, there's an effort to do it in an intelligent way though it often requires some user's input to get a perfect result.