When you get your own chocobo, it's fairly safe to assume that chocobos as an animal come in different sizes, and thus your character picked a chocobo that was suited to their size.

However, Torgal is not a breed of animal; he's one specific animal. I presume that's why the devs made his size constant, because Torgal has a canonical size and thus shouldn't change height based on his proximity to another creature's nethers.