So, the creator made the multiverse serpent to protect this multiverse. The first one. Meaning there is only one in every timeline.
The timelinial ruler came from a different timeline, likely one where the collector somehow died, possibly like a less crazy version of edgyhead but I know almost nothing about the character.
He did not create the timelines.
The crystals came first, which led to the first universe, the creator made the first multiverse. After that, new timelines emerged where things happened slightly differently.
TR came from one of these timelines, just like edgyhead, and all of the other variants of other characters.