All I understand is that you want to boot the second harddrive whilst there is no information what so ever on the first master drive. That is not possible to my knowledge and could be called a hardware limitation. Booting off the second hard drive doesn't mean the system ignores the existence of the master drive. I would be happy to learn other possibilities, because a 1024 cilinder limitation related to booting linux comes to mind, but I'm not sure about the details of this.
Still, a bootflop should work since linux can be booted from any logical partition.
Maybe someone else does understand your question. Good luck with your efforts