Yeah, I figured they were going to do something stupid like this - CA's design philosophy for TW:W3 has been a massive step backwards from TW:W2 so far, and this falls right in line.
At this point, they're effectively removing Isabella from the game if you aren't playing her campaign. The AI is terrible at embedding Legendary Heroes into armies, preferring to waste them on useless campaign map actions. As CA notes, Vlad will be the default AI leader of Sylvania and Isabella will always be a hero. The AI won't remember to embed her into Vlad's army though, so you'll almost never actually fight her in a battle, the AI won't get any of the buffs/bonuses for keeping Vlad/Isabella together, and the whole point of making them a Legendary Lord/Hero team will be wasted.
Personally, I'd be cool with the changes if they could force Vlad/Isabella to stay together in an army and then merge their defeat traits together into one shared trait. Isabella's trait may be strong, but Vlad's is pretty useless.