Talents jumping into Trait rolls is the exception, not the rule.
Bucking is a Special Skill, a Talent that basically serves as a Body specialization. Creative Flair and Keen Knowledge are the corresponding "specialization Talents" for Charm and Mind, and they have similar text for making a Charm or Mind roll when your flair or knowledge would also apply.
In practice these "specialization Talents" will wind up outstripping their root Traits, since only one Trait goes up per level, and you're encouraged to keep them all roughly in balance, while all the Talents you made use of will go up.
Flying is just a Talent similar to Telekinesis, in that it's the default for a pony type, representing something above the body/mind/charm that anyone has. Pegasi wouldn't usually roll Body and Fly to see how fast they can fly, similarly to how Unicorns don't usually roll Mind and Telekinesis to do fine manipulation.
...though exceptions suit exceptional cases.
While not officially supported, the idea can still be there for the cases where the GM's a little on the fence between whether Body or Fly would be more appropriate. Would I let Rainbow Dash toss in her Fly die to Rainbow Crash through a door when there was a great clear straightaway up to it that could accommodate a swoop? Yes. Is that usually how doors are set up? Probably not.
If you've got to cover a long distance at speed, is Body more appropriate than your skill at Flying to coast constructively? If you've got to find your way through a djinni's cloud maze, is Mind more appropriate than your skill at Flying to brute force it? If you've got to impress a Wonderbolt, is Charm more appropriate than your skill at Flying to demonstrate your trickeration?
When the GM's genuinely uncertain, they might as well ask for both, but the GM shouldn't be genuinely uncertain very often.