No reason why you shouldn't ditch the GS rails and fit any other boxes you wish Afterall the BM varios are a bit like an inverted tardis.
There's loads of options from OE ADV panniers right through to Givi's. If you want quality adevnture boxes look at Verns, Caja Sahel (Civils) Stahlkoffer plus others. If you want to spend lots of money on over priced boxes, try Metal Mule and Toura Tech.
Personally I don't think you'll get better, more durable boxes than either Verns or Caja Sahel. Both of whom have mini adds in the left hand margin of the front page of this site.