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They don't get the aura until they are in battle - look at Gumshoos or Lurantis.
I think Totems will be like a little quest. Lana has a raging Pokemon which turns out to be Wishiwashi which you then battle and calm. For Grass we know we go looking for ingredients but maybe we find that the Lurantis has hoarded them all and have to beat it for them. For Normal, maybe in Sun a trainer's Rattata has gone missing at the cave where Totem Gumshoos and its Yungoos allies are, in Moon maybe it's a Yungoos that has gone missing near the cave with Raticate. Like a kidnapped Pokemon situation due to them being like rival gangs.
So there's like a little story behind each Totem that ties into the battle, maybe? I think it makes more sense than having the two aspects detatched and ticking off a checklist of: captain trial done now go find the Totem.
I see what you mean. My suspicion was that a Totem battle would be a prepared challenge assigned to the player by the trial captain after the completion of their trial. This actually brings up the question of just what kind of relationship the Totem Pokemon and the trial captain have. I originally thought that the Totem Pokemon was one designated by the trial captain and then empowered by the islands, but if it is encountered during a trial it seems like islands the have full say over the Pokemon and its role.