Okay i have tested with both minimized to single alias and multiple of them present. When i make a 'startquest <questid>' console call (preceded with stopquest, as it is an always running 'start game enabled'), aliases (no matter how many of them present) indeed do catch all of the fitting refs nearby, be it original or FF-ref. But that is not enough. I will describe in 'expectation/reality' style:
Quest is running, original npc ref appears nearby. Expected: original npc ref gets into alias. Reality: matches.
Quest is not running, original npc ref and ff-ref appear nerby, quest is started. Expected: both orig and ff-ref get into aliases. Reality: matches.
Quest is running, original npc ref and ff-ref appear nearby. Expected: both orig and ff-ref get into alias. Reality: original npc ref gets into alias, second alias remains empty (not filled with ff-ref).
I think you got what i mean. Aliases do not catch ff-refs when those appeared nearby AFTER quest was started, and were not present at the quest startup moment. As the quest is expected to be always running, this will be constant issue for newer spawns.
I have thought of a workaround - making a script which would restart quest on effect start, and applying it to the summon spell mgef. But that is mere workaround, not a solution. Looking to figure out why ff-refs only get caught by aliases on quest init, but not on-the-run.