Some boss makes things unnecessarily complicated. The staff under him has no clue what's going on and is not technical enough to spot this. The whole situation is like the scenario in emperor's new clothes. People run around, taking pride in working on some "noble tasks" and that they are learning a lot. But the truth is: what they did is totally unnecessary or technically sound.
So, do you want to be the child who points out the truth? I would say no if you are a staff to the boss.
Instead, just do what you think it is right for yourself, compromising on some little issues but do things technically correct way on key issues. No need to argue with your boss. No need to point out the truth. Just talk to him about doing things in a "different way" because now you are "short staffed" or "the underlying changing facts call for a change in the approach". He understands what's going on as he is technical. Never let your boss know what he did does not make sense!
Compromise is a skill for people who want to move up. People are not interested in knowing the truth.
The lesson is: as a staff, deep in your heart, you always understand what you are doing and why you are doing the way you are doing. I feel sorry for the officers who labored for "the emperor". They never learned while they thought they acquired some technical skills.