If you install the same app from different sources (i.e. Flatpak and distro packages) and then put Icon widgets for them on the same Panel or Desktop, they'll appear identical. As long as both have the same AppStream ID, in principle this can be known and they'll be visually disambiguated. Unlike the other sub-tasks of Bug 499065, this is harder since each Icon widget would need to know about other Icon widgets it's sharing a containment with. As such, it may be impossible or unfeasible. But I thought I'd open a ticket for this case anyway.