Y have 1Tb external HDD with 3 partitions to test in parallel Batocera, Recalbox and Retropie, this 3 partitions are equally divided in NTFS format each one and identical romset in each one. First partition is labeled BSHARE (dedicated to Batocera), second partition is labeled RSHARE (dedicated to Recalbox) and third partition is labeled PSHARE (dedicated to Retropie). And three microSD cards with this 3 different systems. In the menu of each system is possible to select the corresponding partition to use by each system (but Retropie is a little more complex). So, your idea it's perfectly possible.