Why not just use neurolinks in that case? or clones? We've seen plenty of each before. Genetic modification on a population-wide scale seems like a really complicated way of dealing with that type of problem compared to how Allag has dealt with it before. IDK... If the Allagans are comfortable leaving dragons access to aether manipulation so long as they scramble their brains, why take it away from a population, give them something to make up for it and then just leave everything else the same. Said genetic manipulation can't even be passed down outside the population either...

If Allag was to be the start of the Garleans, I'd almost expect it to be the result of the Allagan version of Malus. That is, the one scientist who everyone thinks is crazy and yet is experiment works. And then whoever is in charge of cleaning up after it didn't quite get everyone...