My eberron game handles fly by having military fortress type places with either a good stone roof or largely underground (if not both) with a simple divination to show the sky above while insideIt's probably best not to think too hard about how Invisibility, Fly, Fireball, Teleport, etc affect technological development, or the wheels will fly off your swords & sorcery game.
Someone complained that EE isn't technically "official", but siege staffs have been mentioned as part of eberron since the 3.5 days & finally have a statblock to provide no more excuse for leaving them out of 5.5/6e phb/dmg again. That it's not official comment rings hollow & shows why the omission is such a flaring problem when they did manage to include this