It's planned in such a way that you only do the preperations pre-time skip, and then during the time skip events you'll fight the war against the other countries on a map similar to the overview map, with the option to use the vanguards and their battle system to get advantages in the war. You won't be able to run into enemy territory with your party during a war.
I think war system could be exclusive to an evil route of sorts. If you go to war with countries you're actively helping it wouldn't make sense. Like, once Varea gets the throne you and Amagal will be allies for life, you shouldn't be able to go to war with them, it would be weird to slap a war system in this already established foundation you got going.