Hm...
The vertical sync difference is right, however you could counter that on windows side using tripple buffer, although this would most likely change the emulation speed a little so its not 100.0% anymore, for example pacman runs on ~98%, neogeo runs on ~101%, although only a REAL freak would notice the difference.
As for the resolutions itself, yeah, MAME on Windows would simply stretch the image (Direct3D) or leave out some pixel (DirectDraw), however as with the vertical sync, I don't belive anyone really notices that.
Also, running AdvMAME on Windows 2000 or Windows XP COULD be problematic, although most users will run it on Linux, DOS or Windows 98.
And if I remember correctly AdvMAME only works with AdvMAME and AdvMESS, no other Windows Software.
The problem with imperfect screen resolutions in AdvMAME you mentioned can be worked around if you tell AdvMAME to only do integer resize.
Maybe in time, I find a way to use the "svgawin" sources to build some minimalistic service so we can use that stuff without AdvMAME.
This would enable a much larger card base to be used, however you would either have to "add" stuff to all common software, or either need to change the resolution (lets say with a batch file) when running special software.
Like I got my windows desktop with 800x600 and say "mapresolution 640,480 512,448,modelinestuff" and once my SNES emulator switches to 640x480, my tool reprogramms the board to the mode I specified.
But thats quite a long road to walk on right now
