They aren't using Allagan Tech. The closest thing they ever used was Ultima Weapon and that was with the help of The Ascians just to even get the damn thing workig.
I thought it was general knowledge that shields typically block unwanted things; Like in any other media or even our own immune systems. The point was, if you weren't an Allagan possess a key, or have a means of generating large amount of aether into a spike(and dragons don't meet either of those crtieras), you aren't getting through. Whats the point of even nit picking something like air being allowed through when we're speaking dragons?
I'll say this again, you're literally grasping at straws just to make a point in your argument. You're coming up with a lot of "but what ifs" which end up retconning the lore that's already in place and trying to attack points that honestly don't make a whole lot of sense.
Dragons have a mistrust of people due to what Ishgardians have done. There ia specific dragon in a side quest that got shot down by an Ishgardian and does not fully trust the player character. Does not necessarily mean they will go out of their way to fight with them, they simply do not have a reason to interact with them anymore (see Hraesvelgr)
Nidhogg specifically has an extreme hatred of Ishgard. He doesn't even simply want to wipe them out, he wants them to suffer. That's why the Dragonsong War was gone on for so long when he could've simply wiped them out. This is the primary reason why the attacks on Ishgard are so prominent.
Bahamut (along with the rest of Meryicida) was enslaved, trapped, and tortured in Dalamud by the Allagans. In FCoB, the game had made it clear that Bahamut has been driven to insanity and blinded rage that by the time he did get out, he's indiscriminately attacking everything. It also does not help that this incarnation of Bahamut isn't even the true bahamut, but just a manifestation of him int the form of an Elder Primal, so it's not even clear if The Allagans needed to be involved to make him the way he is (since Tiamet, his sister, had commented that the Primal they had summoned was nothing but a "crude imitation" of the original)