The whole thing is a Stealth Prequel to 30 Minutes Missions
The girls were being trained to fend off the impending Byron invasion the whole time. Which is why the ones that fell in combat were being kept around, as reserves.Amatsu was the Lady Commander for Alpha Tango before Alice.
Considering that Amatsu resembles an orange version of Alice, it's possible that the appearance of the Lady Commanders depend on the team they are designated to as the only overall difference appears to be color.