So if a horse with Int 3 (can take any feat) was given Improved Eldritch Heritage and 9 lvl perk (can sprout wings for X min/day) would it be considered "flying mount" and therefore not be able to fly in heavy barding? Or since its not a naturally flying mount, like a Griffon, it uses rules for normal creatures (aka nothing prevents sorcerer from flying with this power in heavy armor, other than horrible spell failure penalties).
I would expect table variance, honestly, that's an odd one. I would rule, since it's wings, it would have to follow normal creature with wings rules, so no flying if its beyond light encumbrance, but otherwise it should be fine.
We'll considering that the horse doesn't have levels and probably doesn't have 15 cha it wont qualify for the feat. Probably ever.
In the unlikely event that it does, the GM can determine how they want to run it.
I don't see the source of the wings as relevant. A winged horse with a rider is definitely a flying mount and can't fly in more than light barding (or equivalent, i.e. mithral medium barding), though it can fly while carrying a heavy load (slowly).
(It'll also need proficiency in that barding to avoid taking penalties, unless you stick to armor with 0 ACP, such as normal studded leather, mwk chain shirt, mithral kikko, or nimble mithral breastplate.)