OK this is why I do not use the windows boot loader
first and foremost the windows bootloader uses the Active disk that it sees as the first boootup disk....
the boot record is installed and and that is that....your drive configuration has to stay the same and in the same order so it will boot correctly. so if you had a configuration as such Drive 0 loads the Vista 32 Drive 1 loads Vista 64 and Drive 2 loads XP pro
drive 0 would hold the boot record for drive 0,1,2 with corresponding drive letters C:,D:,E:
SO even if you went into the Vista 64 Registry and fooled it OS see itself as a C: in the boot record it will always be drive D:
so if you removed the current drive C: (vista32) and the Vista64 now becomes drive 0 ....it may not boot or load as it wants to be D: and you have now made it C:
basically it really has nothing to do with the Operating system. it has to do with how the drive sees itself as the Active boot drive
with a boot manager that has a swap drive option it will fool the drive into thinking that it is a drive 0 boot drive. You do this now via the Bios.
each drive that is fooled will load its own boot sector and think it is primary drive ....what this does is separate the drives and makes each OS independently bootable without depending on one drive for all the drives boot records
so as an example you had your drive 0 crash and die on you...you would be able to boot to the next drive without any issues ....if you used the windows boot manager it would give you an error
I view all windows boot managers as limited manager that is only good for booting the OS it resides on.
boot managers are not all made the same and no not always do they swap the drives...usually this is a setting that is checked to work. so you can have a boot manager that will boot to a second drive and not swap the drive and read the boot drive letter as not the primary boot drive
read this as an explanation (it is the xosl how to manual but gives a great explanation of active boot)
it is a bit old but this will apply to any OS with any file system.
just to note: this is for reading and learning...its not really any good for your setup as it still refers to fat tables ans limitations....but is does have some explanation
its late and I am tired so I hope this helps you somewhat...no one is wrong for this type of post and all the ones that reply such as Linney and Wolluf are very smart and give great advice....this is one of those tech gray areas that no one seems to agree on....lol
so I will say both Linney and Wolluf are right and so am I ...so its all how you interpret the info provided.
I wish you luck