I've had both .... the seat bag hitting the back of my legs thus driving me crazier and had the velcro rub my inner thigh thus damaging the fabric of my shorts. The bag I currently have is a Serfas - Mountain Medium (I ride road though). The seat tube velcro strap attaches below my seat post collar and that adds additional protection against the velcro rub. That is a factor of my bike's configuration as others have noted below.
Susan
Try not. Do or do not... there is no try.
Yoda
2004 Airborne WASP (road)/Selle An-Atomica
2010 Bike Friday New World Tourist (commuter)/Selle An-Atomica
2010 Bike Friday Pocket Rocket Pro/Selle An-Atomica