I found the same thing, the BMW adaptor put the position of the top box too close to the rider, so I made an 'intermediate adaptor plate' of my own to mount it a little further back... the top box now has about 150mm of 'stretching space' in front and is flush with the tail light at the rear... I never did like the box hanging way off the rear of the bike anyway, I'm sure that there's a certain amount of 'pendulum affect' on the handling... I'm all for 'Mass Centralisation.'
I extended the front seat to cover the exposed portion of the bike to give a sort of 3/4 length single seat... very comfortable.
I changed the BMW adaptor plate for a universal Givi one after the BMW top box fell off in Romania, no surprise on those roads, and used a Givi E50 box until I sold the bike and had no problems with this at all.