Just did some testing with overlayfs, in the hope that maybe NTFS or ExFat would support the needed features.
Overlayfs refuses to mount Fat32 (Through vfat) filesystems even as a lower directory...
It can mount exFat and NTFS filesystems as a lower directory, but cannot use them as upper directories...
(Lower being read-only directories or devices, Upper being where changes are written back to..).
So right now if you used OverlayFS on any of the common Windows filesystems you wouldn't be able to store things like config data for a pnd in the /media/SDCARD/pandora/APPDATA/APPNAME.
There's probably some clever way you could deal with that issue, but if AUFS works it's probably the better call. Additionally AUFS appears to still be compatible with the latest Linux Kernels so I don't think it'll cause any potential upgrade problems, at least for a while.
That all said.... I think Flatpack, or possibly Snapcraft could be worth looking into for packaging systems, or at least be worth studying for features for DBP to support...
If I get really motivated about it, I will see about contributing to DBP and could research adding the option of it supporting OverlayFS mounts when the underlying filesystem can support it.