Dellis,
I have went for the touratech option on my 1200gs. If you buy the bits individually, not as a mounted set, you can mount your boxes in any position (within reason), so the pillion will have some leg room. Its just a matter of mocking up.
Once your happy with the positioning, you can mark up the holes for drilling and mount the quick release hardware.
Im overseas at the minute or i could have posted a photo for you.
Hope this helps.