It may possibly be possible, maybe, that killing more mobs during a dungeon instead of skipping parts of it grants you more "light" for your Nexus weapon than speed-clearing it does.
It could also be the other way around (i.e. really fast clears reward you with more "light" than full, take-your-time clears). Or it could even be a combination of both. More testing is needed.
Edit: YES, they MUST nerf Atma. I am absolutely appalled that they still have not done so. The fact that the later phases of the relic quest are less arduous is cold comfort to those players still stuck on the first phase (as well as players looking to upgrade their relics for other classes).
It could also be the other way around (i.e. really fast clears reward you with more "light" than full, take-your-time clears). Or it could even be a combination of both. More testing is needed.
Edit: YES, they MUST nerf Atma. I am absolutely appalled that they still have not done so. The fact that the later phases of the relic quest are less arduous is cold comfort to those players still stuck on the first phase (as well as players looking to upgrade their relics for other classes).