Hi AT, the only reason I can think of is they are being cautious about excess hydrogen being given off in the enclosed environment of the boot during the rapid charging that happens when jumping, and sparks from the jump leads setting it off. Possibly they also feel you'd get a more direct connection when the battery was low by excluding the car's battery cables.
Otherwise, electrically, it would make most sense to jump battery to battery imho as the terminals under the bonnet can only be parallel connections to the battery posts.
I did google it as it got me intrigued (I had a BM with battery in boot but never even saw it in 5 years). First thread up more or less says no problem either way but I wouldn't hook up negative to the bonnet hinge like one poster there or you may find it welded up http://www.bmwland.co.uk/forums/viewtopic.php?t=107261