So I think that is enough evidence, at least to me, to suggest that the game automatically applies buffs or debuffs to objective completion without any regard for player participation. Most likely under the guidance of AH employees.

The defense rates aren't static. Enemy forces have weaker resistance as a planet's liberation progresses. We saw this demonstrated in the recent dark fluid missions where this modifier was scaled a bit more heavily than usual as the entire community was focused on a single planet. It results in a bit of a snowballing effect, where it's initially very slow to liberate, but then picks up speed very quickly.

Of course, Joel could be putting a finger on the scales, too. But I feel like whenever they give us a choice like this, they seem to leave that choice and the consequences of it entirely up to us. They tend not to give us choices at all for the things that play into the bigger narrative, which this mission doesn't really appear to be.