edit: not sure if possible, or how to make it so not fiddly, but methods to disrupt enemy quests?
Perhaps by way of a competitive quest, similar to the ones in Endless Space 2, which I've seen you fiddling with recently? That is to say, a Quest which all players they are positively affiliated with know of, and must compete to finish first for the reward.
For example, the Autonoms asking their related players to eliminate inferior biological units, or flip that around to eliminate mechanical units for parts. First player to destroy(disbanding doesn't count, or it could even be an opportunity cost option!) either a raw number of units, or a certain value worth of units. Either a simple 'each tier is worth 1 point,' or more complicated 1/2/4/7 T1/2/3/4 point value system. These units could be independents, or opposing players. They don't care!
They may offer a consolation prize, but I think first to succeed gets all the reward is good, too.
Some other faction requests the research of either a raw number of techs(more fair between different research values), or a raw amount of research consumption. First to reach said number wins. I favor the raw number of techs approach here, since somebody with less research, might still be able to win if they at least have enough research to get some lower tier techs done at a competitive rate.
The extra benefit of this one, is to a lesser degree, even if you don't win, you at least did some research, even if it might not have been what you originally were going to spend that research time on(also an opportunity cost here, depending on the potential quest reward).
Heck, they could even ask players to dedicate research towards a dummy-tech theoretical research, with the winner perhaps getting some research points at the end(not as much as spent), along with another reward on the side. Which would be a true opportunity cost. Research whatever you were going to that gives you direct unlocks now, or put time and research towards the quest, potentially getting nothing(maybe) if you don't end in first place.