You are right, it doesn't allow fitting of the top box whilst rack is fitted - however it takes only minutes to fit so if you are going on a trip you could always swap between the two. Top box on its own for short trips near home - panniers and rack with tent etc for longer trips.

Alternatively GasUp has adapted a rack with some plastic blocks shaped to fit the top box receiver on the bike - that way the rack slips into place like the box would, though i dont know how it locks into place. Darren - pics?