The only major thing that would need to be changed is the books for the ARR relic weapons that require open world Imperial soldiers (which proves that the entire thing is a scam anyway, since no "ancient tome" would ask you to kill members of an occupying force that has existed for less than 20 years) and any hunt marks or hunting logs that call for them. That said, the amount of recoding required to have the Castrums switch to "empty mode" after you pass a certain point in MSQ, probably during Stormblood, would be more trouble than it's worth. At this point they have the technology to change the zone itself depending on your progress in MSQ, but mobs appearing or disappearing requires specific flags and I don't think it impacts any of the open world mobs. So recording the Castrums to not be crawling with foot soldiers would be such a major undertaking...... I can see why they felt it was easier to simply leave them be.

That said, if Garlemald is ever defeated "for good" then it might be worthwhile to figure out whatever programming trick they need to have the abandoned legions finally pack up their bags and go home, and have the relic or hunting logs spawn only the needed soldiers in the area until those flags are cleared.