These fights are still current content, SE wants you to be using those totems on weapons etc. right now while the content is current, and for you to keep the content queues alive by continuing to farm in the hopes of getting the mount.

Basically the 99 totem thing is staggered to encourage players to do the content when it is no longer relevant. It sucks for you to not have the mount after 99 runs, but the game design is sound.