To start off I don't know how Bradford and Shen even found this ship and managed to get it working without the aliens finding them, if they wire there own weapons to self-destruct upon death you would think they would want to recover a downed spacecraft. But that could have a plausible explanation so I will let it slide. What I won't accept is that this is established to be Xcom's primary base of operations. It is established that the aliens have already conquered the world and we are a resistance force, so wouldn't it be fairly easy for the aliens to track the avenger and shoot it down? Keep in mind in the first Xcom our current tech satellites had the ability to track the aliens advanced UFOs, so why couldn't the aliens do the same with the Avenger? Okay maybe the Avenger is a special kind of ship that is able to evade that kind of scanning, (kinda calls into question again how Shen and Bradford were able to get the ship, but again I will let it pass.) But it is also established in Xcom 2 that a UFO could track and bring down the Avenger, so why aren't these UFOs running around the clock hunting the Avenger? It's not like in the first game where they were invading earth, they literally control the whole planet. They would be able to run UFOs around the clock to hunt the avenger down.
These needs explain why retired Avengers systems in storage have been rehabilitated and sent to new active duty units to provide air defense to the maneuver force. These avengers are a stop-gap however as they are extremely vulnerable to enemy direct fire weaponry since they have no armor. Even in the Gulf War, Avengers were put in semi-permanent prepared positions behind earthen bunkers to protect them from crude Iraqi tanks. As Avengers roll out, new IM-SHORAD Stryker-based platforms will fill in behind them to fix the issue of survivability. The advantage of having these Avenger battalions set up now is that the IM-SHORAD systems can fall into formations waiting to receive them.