The origonal reason for the crossovers, or pre mufflers, was to enable more restrictive, read quieter, silencers to me fitted without loosing power, but over the years they have grown to be credited with supernatural powers, so expect the " experts " to chime in and tell you that you will create all sorts of problems with your engine.
Main problem will be that it will be a little noisier, and if you put on a dyno it may even be possible to measure a small loss in power, but probably only over 6000 RPM. But you still have the front pipe which should help.
Whether you would notice the difference on the road is another question - my GS runs better without the rear box, but I have a freer flowing Staintune can , I have heard that they struggle with stock , and no front balance pipe.
Adelaide Hills, Australia. 93 R100 GS, 77 R75/7 ,70 BSA B44VS, , 86 R80 G/S PD, 95 BMW Funduro F650 ST