Excellent idea. I have an alternative incorporation for it though.
After alien crash lands this new mothership is searching for him. It is high in the sky in commonwealth and occasionally despawna and respawns at new locations. Only way to get there is by Vertibird. You have to discover it each time to gain marker to land on it. It is so high you cannot see it on ground unless night time where it has a strange light.
Flying up via vertibird will. Mothership fire at you. Repel and take down turrets with machine gun and land in the hangar bay. Destroy it by placing a charge and jumping out with power armour or getting picked up. Kaboom.
Multiple motherships spawn