I think there's a thread about this here. There should be nothing to prevent that. If the drives are not connected at the same time, they don't know about each other and therefore think they're the only drives available. If you don't switch any hardware parts (except the HDs), the system stays the same for each OS. If there is only one drive connected (powered etc.) at a time, BIOS should not mess up with the configs either (it's possible with a two-drive configuration, where both are connected and then one is removed and re-plugged or fiddled with in some other way, that BIOS and bootloader notations about the drives get messed up too, preventing you from booting before fixing it).
Go ahead. Have one drive connected at a time, install the operating systems as if the disk was the only disk in the system..and never plug them in at the same time, to make sure no trouble pops up