Upcomming missions in TWoS are independant, wether you return to port or not, wether you take them at the bunker or not. Missions have a timeline and that's it. So you can pretty do what you want (what counts for your career is the tonnage, not the mission).
If you don't want to miss a particular mission, just be sure not to stay too long in port. The KSD Commander can help you for that, also there is a separate mod called 'Change Days In Bunker' that you can load to exactly set the days in bunker.
Same goes for historical encounters btw, just be at the right place at the right time.
Only time where you really need to pay attention is towards the end of the campaign chapter, but then you will get red messages. Always read and follow red messages
