Coming on January 1st, 2018, there will be another change coming to the Command Mission Team:
One Navi per Member per Month can do battle with the Boss Team.
This means that if I have Kajira participate in a team to take down the CMT in January, none of my other Navi can participate in a CMT battle for that month. Other boss battles are still completely open and available but at this time, our activity is higher than it's been in quite some time and as such, the influx of Exp and Zenny (and bugfrags) to be found here has been decided to be a little much.
So if you want all your Navi to make it through a CMT run, do it in December.