1. Why doesn't Rarity have defeat detection for Ashes of Al'ar, Swift White Hawkstrider, or Smoldering Egg of Millagazor?
Rarity's defeat detection doesn't support having a boss in two places at once simultaneously. Kael'thas Sunstrider and Ragnaros exist in two instances at once. This is a known issue.
2. Understandable request. Reins of the Crimson Water Strider and Bristling Hellboar for example are part of rarity and they both are vendor items.
On the other hand look at your tooltip. It only shows the mounts and is already huge. Now imagine all the 50, 100 or even more reputaion mounts, pets and toys were added.