Wouldn't be weird at all if that's the case.
I mean, considering "Everlasting Saga" seems to be soon after the princess game ends and it's about her nation entering war, would be weird if she wasn't the protagonist x)
I wouldn't base things about the logo tbh, it doesn't mean much at the end of the day. Also i mean, even if it will be an important event, the reconciliation that can happen between Priestess and Kirstin, it's less important that the friggin war xD
Also yes, seems to be this, that you're playing at the side of the princess and that the Empire Kirstin is part of is the enemy. And we know Fire Emblem games, wouldn't be the first time you can recruit an enemy, heck Sikorsky already teased you can recruit enemies (grunts in this case outside of story) so xD