They definitely overlooked it, imo. Originally it was intended that you would wear the level 45 stuff along w/ the 50 chest (because you didn't have access to better gear at the time) to start going into dungeons (wanderer's palace + amdapor keep) to start getting gear upgrades.
Them adding the full i90 set completely ruins that, so they definitely need to go back through again and fine-tune things to make more sense :\