as far as i know, no.
live area bubbles are shortcuts to their apps stored in ux0:/app/(app id), ur0:/appmeta/(app id), and ux0:/appmeta/(app id).
for example, retroarch would be ux0:/app/retrovita, ux0:/appmeta/retrovita, and ur0:/appmeta/retrovita.
if you want two versions of one app, you'd have to edit the vpk to create a new directory in all three locations.
if you can do that, then do it.
otherwise you'd need two different consoles, or just stick with one version.