Just confirmed: "On Auto" missions do not require auto the entire time.
I can't auto through FK Hard and I'm on the Marius mission to finish that battle "on auto" numerous times. I just tested it. I started the fight on auto to get through waves, shut auto off for 95% of the boss, turned it back on to land the killing blows and I got credit towards the mission.
Hopefully this is helpful to someone for this one or any other "on auto" mission.
