If we're focused entirely on airborne targets, Flakkson's rune of Seeking was designed specifically to hunt down dragon riders and makes shots more accurate against anything that can fly. The Rune of Penetrating can increase the strength of the bolt hitting the dragon making it more likely to hurt whatever it's hitting. The Rune of Accuracy does the same thing as Flakkson's, but can be applied to anything and can stack with Flakkson's rune. A Master rune of disguise could be good if you want to hide the Bolt Throwers from aerial targeting/sabotage. Other than those I don't think there are super useful engineering runes.
Edit: Specified what The Rune of Accuracy stacks with.
If it's disguise we're interested in, we could probably make a tarp or camo netting enchanted with Invisibility or Take No Heed (or some other spell) to hide the bolt-throwers or cannons while also freeing up a rune slot for the artillery pieces.
Alright, I tried keeping up with the conversation but the thread moved too fast for me to reasonably follow and go about my daily life, so I skipped more than a few pages. In the interests of contributing something hopefully helpful, here's my thoughts on the defense tower;
Tower of Thunder: Lightning tower, can cycle between low key thunderbolts, chain lightning vortex stuff or Urainnen's Thunderbolt to cover most of your damage-dealing bases.
Tower of Gales: Winds tower, uses both the lore attribute of Roiling Skies to harass enemy fliers and can produce most wind-based effects like Wind Blast or just help give friendly fliers a nice tailwind to help them keep the mobility advantage.
Tower of Portents: Divination tower, all the omens and portents and other such fortune-telling effects, useful both for daily life and laying down benedictions and maledictions where necessary in the heat of battle.
Runic battery (bolt throwers, cannons etc with runes engraved on them for specific damage-dealing potential, probably the more mobile of the artillery platforms). Seems like something that is best handed over to the dwarfs, both engineers and runesmiths.
Engineering battery (manling guns with lots of powder and shrapnel, manling crewed but probably with engineering guild involvement in their placement) For a blanket 'to whom it may concern' artillery cover. Should help best against things like harpies, but here we can probably risk a degree of magic nudging specific crews to higher performance either through a separate tower or a magic item, like a crown of trial & error for the best manling artillery commander or something.
The three towers are meant to be chambers in a Blue Tower that synergize with one another, not 'these are your three options choose one'.