Practically this only concerns Teemo, because all other stealthed champions don't really use Aery or Arcane Comet (LeBlanc does but this scenario is irrelevant... maybe Shaco AP).
Using Teemo's passive wisely is a key part of its kit, while Aery or Arcane Comet can trigger on nearby enemies and thus revealing his position. Stealthing on the midlane with shrooms around is likely to happen (and should) in the late game, and at this point you'd just hope your rune was disabled. I believe poor Teemo was omitted while designing the Runes Reforged.
I'm not yet sure whether this problem is about stealthed champions, or rather about any champion that is currently not visible on the map (e.g Nidalee stealing enemy jungle camps, her trap would trigger an Arcane Comet that would reveal she's somewhere in enemy jungle). I'm not fond of this alternative, but I just write it down for the sake of brainstorming