I have no idea how Windows addresses multiple drives. (The letters C:, D:, etc., refer to filesystems, not drives.) My guess is it would do the same as GRUB, and that they are getting the switchover from the BIOS; and I would guess that the Linux kernel accesses the hardware directly and so has no idea that the drives are flipped in any sense. It just knows how the hardware is set up.
My handwritten GRUB2 configuration sure is faster than the one generated automagically by Ubuntu, or at least I think this is the reason for the speed increase. I think the automagical settings could be tuned for speed, however; the default seems designed for removable drives showing up who-knows-where and having to be found by asking them all for their ‘identification papers’.
