An issue is that mission as defined by the Traveller setting differs from mission as defined by High Guard. High Guard gives us a fundamental mission: win the battle as defined by the design and combat rules. Achieving that mission doesn't generate the ships that the setting imagines for its missions. One resolves that conflict by either prioritizing the High Guard mission and forgetting about the canon ships or prioritizing the setting missions and accepting that the resulting ships will be a good deal less than optimal.