Versus the Enclave retaking the base or someone else. In any case, the Battle was still ongoing when it happened and only destroying the Mobile Carrier makes sure the Enclave knows it's defeated. They could have counterattacked and used those missiles.
I also think those were the only missiles they had left.
Come on, the Enclave is pretty much destroyed already even before we invade the base. The BoS say that they are just the last Enclave troops left and when the Lone Wanderer attacks the base we see BoS troops mopping the floor with Enclave troops all over the base. I doubt that after the Lone Wanderer takes control of the Base (and if the BoS occupied it) the Enclave has any chance... Remember, they can't come in Vertibirds to attack the mobile base because Tesla Cannons, and would be seen miles away if attacking from the ground.
All of that was captured. The Mobile Carrier is just a missile platform.
Wrong. The mobile base crawler is the new Enclave command center and it has the base floor which consists of an engineering bay where they repair robots and other stuff like weapons and armor. The second floor contains a laboratory where they research deathclaws, a big medical bay with several rooms, toilets, a dining room, a kitchen, barracks for a lot of personnel (sleeping quarters), storage area/armory and a robot control terminal. The roof has Vertibird platforms that can be used like a carrier transports jets, several defense turrets and access to the satellite control tower (which on itself contains three floors).
It is a Mobile BASE Crawler.
They have everything at Addam's Air Force Base. The Lone Wanderer, who is not the BoS anyway, is the one who blew up the Mobile Carrier after sneaking onboard/shooting his way in.
Again wrong, they do not have a giant base that can move by itself and is so advanced that even Rothchild says:
"I've been amazingly busy ever since we began clashing with the Enclave. All their technology is amazing. It's going to take me years to sift through the wreckage of their mobile platform alone. I suppose we have you to thank for that."
Also the Lone Wanderer is part of the BoS.
The Lone Wanderer becomes a member of the Lyon's Pride during the Take it Back! quest and becomes a Knight in the DLC Broken Steel (and the game even assigns the faction BoS to the player, we used to have a problem in early TTW where the NCR would be hostile against the player if they had started the Broken Steel DLC before going to Vegas because the game made them a BoS, we had to create a new BoS East Coast faction and assign that to the player to fix the problem).
They'd move very very slowly across rough terrain?
We don't know how fast it is, what if it is really fast? We never see it moving. For what we know it might even have rockets and float like a Mr Gutsy/Handy.
And what
@Walpknut said I guess.
I don't understand this fixation of Bethesda to make BoS destroy all the tech that is more advanced than the one they possess when they can take over it as easily as destroy it...