Yuguri says hi. And even then, Au'ras being playable at the beginning of 2.0 (new adventuers are either legacy players thrown forward in time, or returning/arriving to Eozrea from a previous journey) makes a hell lot more sense than what you're trying to suggest (with Cid somehow uploading a virus to an allagan construct when you don't even interact with Cid until half way into the storyline, let alone in the beginning, on a creation that has long existed and probably gone into deep sleep before Cid was ever born, let alone even get in contact due to the events of 1.0 transitioning into 2.0 and his amnesia). The matter of fact is, iand is even mentioned in game on multiple occasions as well as the binding coils, that the allagans are in a far far more advanced state of technology than even the garleans can ever hope to achieve.
The burden of proof is on you to to make a case of lalafells or miqo'tes being created by the allagans, because you're the one that's trying to make a point that an allagan-synthesized race is feasible from from a story point perspective (unless you want to give them exclusive MSQ) from the ground up.
Remember that we have different factions of dragons. Nidhogg specifically has excess rancor toward Ishgard (not elezens, don't mix these two together) for their betrayal. Bahamut has been driven to insanity by the Allagans and their inhumane treatment and imprisonment of the dragons of Meryicida. The Allagans are objectively immoral people with their experiments and ultimately causing the Fourth Umbral Era, a point that even Y'shtola agrees on during your quests in Ayz Llya. Even if there were any true allagans that were somehow alive, I'd doubt anyone would want anything to do with their schemes, let alone work with them.I think that.. is the opposite. If the Dragons had such a bad time against the Allagan constructs why would ALL OF THEIR DIALOGUE be about the Elezens and how they betrayed them. WHY would they be throwing all of their forces at Ishguard trying to wipe them out instead of wiping out the remaining Allagan things. It was obvious and it is obvious the Dragons know where they are, and it wouldn't be hard for Dragons to ask their multiple sources to create something to gain access to that Island, in fact there are creatures on it. That shield wasn't unstoppable.
The Dragons seem to hate Ishguard and Elezen more then anything. Why else would they throw almost all of their hoards at them?