Under each location, there are these little symbols that look kind of like stylized flames. They seem to be lighting up as I proceed through the areas but I can't figure out any 1:1 relation for them, and the manual and Datalog are useless here. What are these actually for?
They correspond to the number of gates in the area:
Because you need to unlock gates as part of the main storyline, you'll undoubtedly have orange gate icons for most of the locations by default. The other ones unlock optional paths and are usually unlocked with wild artefacts found in optional parts of the area.