vgm is not only for the megadrive system. It can handle several other formats, such as master system, adlib, neo-geo etc. Deflemask is a tracker which can export to several platforms, in vgm format (not all vgm players can replay the newest specifications): http://www.deflemask.com/
(sadly, you can't create tunes for the ST / ym2149 chip, maybe one day...)
See vgm as a container. Like the YM format, it contains instructions for how to send data to the chip (through registers).
VGM is also supposed to handle the MSX sound format. They had several chips (AY-3-8910 and later ym2149 like on our ST, and on MSX2+, FM chip like YM2413). So maybe it could be possible to do something with it, but I don't know if it worth it, because it would only be useful for modern VGM player on your PC, where you also have plenty of YM players. If you intented to play YM files (or other format) to a console VGM player, on your megadrive for example, it wouldn't work anyway because it's not the same sound chip. On my Megadrive I can replay only VGM I made with Deflemask targeting the Megadrive, of course.
About YM, I doubt you could record / save music in YM format if you play it from SNDH. I would only work for game using more classic music. For example when recording the Xenon 1 music, a (spoken) sample was not recorded in ym. I guess it's the same for sndh. And no, you can't modify a YM file, you can't extract music and such, unfortunately. If you want to redo the music into another tracker, you can only do this if you can get the original source of the music (or by ear).