Your commander in chief doesn't care if you are in port, but he'll care about the target not destroyed in the given timeline. Go play Jane's 688i, if I'm not wrong there is an angry looking chief-commander who shouts at you for 1 minute, you wished you were not there...
(I think I get this vid in CW as a mod for more immersion...)
Missions have a fixed timeline. If it's over you fail mission. Simple. It's your job to synch it well and this makes it more challenging IMO.