I'm starting to think that it might not be based of level, but time.
For instance Aglaia is level 90, and take less than 20 minutes, but Nier (Tower of Paradigms Breach) is level 80 but take over 40 minutes. Aglaia give about 550, but Nier give 999.
The completion time is pretty much twice as long for Nier even though it's a level 80 raid, and you're given almost twice as many points (i'm guessing it's capped at 999, if you exclude the daily bonus).
And because Normal Raids & Trials usually can be completed in less than 10 min, they award you with less points, meaning you'll max out High-level Dungeons & Alliance Raids quicker since you have to do fewer runs.
Without the daily bonus.