The bot dismounts before several actions to increase reliability. The bot is not designed to be the most efficient means of performing a task. It is designed to perform tasks successfully. I'm sure the developers would be willing to dedicate time to performance optimization once the bots are 100% reliable, but since Blizzard is constantly patching the game and requiring Honorbuddy and all of the associated plugins and profiles to be rewritten I wouldn't count on it. Performance optimization is likely not high on the to-do list.
There are issues with quest turn-ins and pickups if you are mounted. Some quests cannot be picked up if you are mounted, and being mounted can cause you to be out of range. Also, with flight you may not be on the ground when you arrive at the coordinates. There are a lot of potential issues that can be caused by being mounted with turning in/picking up quests. It is easiest to just have the character dismount before trying to attempt these actions.