Asahi showing up in Varis' stead isn't a problem. What I more have a problem is is that I can't think of a way the Scions (or the Alliance for that matter) can verify that he's presenting what Varis' stance on certain topics actually is. As in, what's to prevent Varis from telling Asahi that certain options are on the table when Varis knows they aren't? Everyone kinda has to take Asahi's word for it that he's presenting Varis' stance accurately and there's so many ways that could go wrong I really don't see any good reason to trust him.

Another group that Varis having an alliance with the Scions/Eorzean Alliance could cause a lot of problems for: the Garlond Ironworks. Forget Cid (and Nero), most of the people in the Ironworks are people who escaped with Cid from Garlamald (this includes Jessie, Biggs and Wedge). As far as how bad of a problem this could be for them... most of the Ironworks employees (especially the ones from Garlemald) use fake names so that the Garleans have a harder time figuring out who in the Garlean Empire they can use as blackmail against the Ironworks...