How do I engage the Enemy if I am in my Fort ???

[Taqwus]

It's not unusual to have commanders which you -don't- want participating in the battle -- ex. researchers. In addition, this forces you to choose how they spend their time -- which is not completely unreasonable.

It's also quite possible that you'll only have a force sufficient to hold the walls for a while, and rely on a mobile, nastier, and probably much more expensive force to break sieges. In a multiplayer game, you might not want to reveal everything you have inside a fortress to a single probe...