How will the self-destruction feature work in the Ironclad? Can I initiate self-destruction in the command module and detach to fly away, or will the command module also be in self-destruction mode?

There are two independent self-destruct systems, one in the command module and one in the main hull. Setting it off in the command module will self-destruct both (if attached), while the main hull of the base ship can be triggered from the control room.