First, most emulators cut off the top and bottom EIGHT scanlines, not SIXTEEN, leaving the 'effective' resolution at 256x224. The only reason they do this is because on most NTSC television sets, the top and bottom 8 scanlines are covered up by the frame around the picture tube. They're still rendered (and will trigger sprite 0 hit etc.), but you *usually* don't see them.
As for my reasoning for putting vblank at the *end* of the frame rather than at the *beginning*, the main advantage is that it makes PAL emulation a WHOLE lot easier. Allow me to demonstrate:
VBLANK first: NTSC - VBL=0-19, SCR=21-260; PAL - VBL=0-69, SCR=71-310
VBLANK last: NTSC - SCR=1-240, VBL=242-261; PAL - SCR=1-240, VBL=242-311
As you can see, it's a lot easier to just say "the last scanline of VBLANK is either 261 or 311" than to shift all of the numbers around like that.
P.S. If you don't get this note, let me know and I'll write you another.