Well, we know that the Warrior of Light canonically charged into the Castrums to literally infuse a weapon with the souls of those slaughtered and that such an event took place after Gaius' defeat so whilst some Eorzeans may very well allow the Garlean remnants within to do their own thing I doubt it applies to everybody. As for Varis being 'fine' with how the military operates I doubt it very much - we know he spoke up in defence of Regula and was firm friends with the man for roughly thirty years so I doubt very much that he approved of some of Regula's own men betraying him. We also know that he sees his own heir as a 'monster' so clearly he did not approve of Zenos' actions either. Furthermore Varis was against the Meteor Project.

He's also but a single man, Emperor or otherwise. By all accounts Garlemald is a vast and powerful entity and different elements of it operate independently of one another. He also rose to power through a bloody power struggle which is unlikely to have ceased completely. Funnily enough, I feel that Gridania's leader can be quoted to attest to such a fact: