From what Andy told me, it doesn't matter if you write your own ini's, cos the resolutions the AVGA is capable of are the ones it'll do. That's why, for example, anything below 240 isn't supported; it's covered by that resolution.
Yes, hwstretch off. However:
1) you'll still need to use the monitor OSD to size games. You'll have to find resolutions per game that coincide with other games' resolutions.
2) vertical resolutions aren't hard to find; except for odd games, like Strikers1945 or something, most are selectable within the avga's parametres. This is why I use Mame32, cos it's easily accessible, particularly in a graphical format. And though some say there's a performance hit if using an FE, I haven't seen it. However, if you'd rather use cmd mame, use mame32 to set and test ini's, and then copy your ini files over to the cmd mame directory. And there's no reason to have different versions of mame for different game settings. That's why they have discrete settings, yo. In a case like this (native resolutions), the majority of global settings aren't relevant.
Supplemental: some games require different resolution settings depending on the orientation of your monitor. And, in some cases of vertical monitor orientation, image sizing via the OSD is still required.