From what I have read I suspect this may have been an intentionally created incompatibility. They wanted dual boot to be inconvenient. As a user, that is not the sort of design I want.
But if the user prefers some other bootloader instead of Microsoft's or Apple's, then all bets are off. The idea of the "primary" OS being something other than Microsoft's or Apple's is not contemplated. For me, the non-GUI OS is the primary OS and the GUI OS is something kept around out of necessity, only used occasionally.
