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In a game with a lot of Factor interaction, since they are a hive mind the reputation rules apply perfectly to them.
I think that any organism with a set protocol of interaction, would be candidate for reputation. Relative to transhuman social interactions, though I don't now how recognizable it would be to us. But I see where you are going with this idea. Not bad at all.
Of course, it wouldn't be called Reputation. Factors might call it 'Utility', and measure it on your possible use for their purposes. Or maybe 'Reliability', and lower it for mucking with gates or AI.
you're supposed to add new reputations as needed, when PCs are dealing with any particular faction that falls outside the predefined groups. If you were playing a game that dealt heavily with the factors, i'd say you should write one in for just this purpose.
calling on them for favors might be a pain though. wait 3-5 years between visits, or whatever its supposed to be. might make for some interesting long-term background projects to run in tandem with more traditional operations, though.
If you keep their visits to that schedule, making a rep for them is probably more than is needed. On the other hand, it would be needed if you:
-Stepped up the frequency of their visits.
-Gave them a permanent presence in our solar system.
-Had their ships leave behind large Q-bit reservoirs for emergency contact.
-Discovered a pandora gate destination close to one of their worlds.