Just like the entire game where your choices mean nothing. This is a themepark MMO, were you expecting something different? Get used to linear questing and progression. Sad but true really.
Things MIGHT get mixed up when they add new primals and the existing HM primals become optional content for people relic hunting and they add new dungeons and such. But if they tie the HM primals, Extreme primals, and the new dungeons to the main storyline then you can forget even that.