You need it up the whole time. And it need to be up before you activate the voyage and you cannot change it before the voyage is completed. Not even to make alliances. Or else it won't count.
About the PvP for the reaper flag, you can forget about that. Nobody is going till you because of that. Since most of people are still trying to complete the legendary commendations.
At least it's been my experience so far and I've already completed all the commendations.
People keep friendly, wanted to test the cursed in a friendly way without fight.
I've only encounter 3 hostile crews so far. And it was in the beginning so probably they wouldn't even aware of the new features and adventures.