My 68 327 (not RS) has original a/c. The heater hoses do cross over like D5 shows in the 68 AIM. So, I think Paul (and the AIM) is steering you right.
When you use the hose clip to the compressor, they pretty much have to go that way. You are right, it does look a little "twisted", but I assume that's to keep the belt and hoses apart.
Also, the AIM does not show an a/c hose clip for the inner fender on D6. Mine does not have one and there is no second hole on mine for one to clip to. If you guys find there is supposed to be one, let me know!