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Does android do any maintenance whatsoever on stored data within /data or external sd? So if I have an app installed on 1 system and not on another system will android see it and clear the data?



No, all storage partitions are shared between ROMs. If you installed an app, it'll be availabe for all of them. Since on locked devcies we're limited to stock manufacturer-based ROMs, this makes the switch between ROMs very convinient (you don't have to worry about your changes/data/setup & storage space on the another ROM; all ROMs share everything except system). However, you should make regular backups in case a virtual ROM (probably with unsafe mods) results in bootloop due to your user data. In this case, it's safe to wipe data & selectively restore apps/data from backup(s). Another advantage of sharing all storage partitions is that your messages/emails/etc received on a virtual ROM are immediated synced (actually shared) to the other ROMs.