Welcome to the word of balancing
If we make the raiders too tough, players instantly die, etc.
If we make the Theseus too weak, with persistent damage people fail M5 through no fault of their own, etc.
So overall yes the baseships are weak and the raiders are weak. Intentionally. The idea is to capture the feel of the show and Galactica goes through a lot and we didn't want to frustrate new players even though we hit the "missions can play themselves" issue in a few places.
The Raiders and baseships in the campaign are weakened by a huge degree. The default loadout for the baseship can give the Theseus a pretty good kick in the teeth.
The realistic amount of Raiders would be... 784 or so per baseship? (I think that sounds right for the rack figure) Even if they launch half of their wings let's say it'd be crash ville far worse than the stability issues some players are currently having.