I believe the duration is for however long you are in the zone, but that doesn't matter here.
Let me put it this way, if you cast alliance on one npc then on a second npc, it can absolutely change the faction of the first npc. It has happened to me several times, and my friend has experienced it too. I assumed this meant it applied to one npc at a time, but as I said I could be wrong.
Zero impact? If what I say is accurate, which is might not be, then you could have modified your faction by casting on a second npc. Just trying to be helpful, good luck tho.
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