Yeah, the Allagans were still explicitly at war with beast tribes during their day, most notably the beast tribes in Meracydia. It's unlikely that they were the progenitors of all the beast tribes, especially with the consideration that enough mastery of aetherochemistry to be able to create Chimeras was only possible near the end of the Empire. Amusingly some Eorzean scholars believe that the Biloko line of enemies (the tree people) are actually the Meracydian tribe that summoned Sephirot in ages past. But they're not even considered fully sapient anymore.