I mean, I'm equally of the opinion that elves wouldn't forget how to use a longsword when they polymorph, nor would a non-elf suddenly learn how to use a longsword due to polymorphing into one. The reason for this is simple, the elves' proficiency comes from a cultural training they have through their upbringing. This is something that makes no sense to gain or lose from polymorph. Just the same, the human's bonus feat comes from the fact that humans learn quickly. It makes no sense for something you learned to be randomly forgotten simply because you polymorphed. The whole point of polymorph is specifically that you don't affect the mind with the transformation.
As to why I mentioned balance, it's because someone else did, that it was a balancing factor because other races lost physical qualities like low-light vision and whatnot.
On a side note, can someone actually point to where it says the human bonus feat is an extraordinary special quality? Because I've never seen anything of the sort. Both the bonus feat and the bonus skill points are listed under human racial traits in the player's handbook, but are not mentioned anywhere to be Ex, and unlike the other races, humans have no monster manual entry that can clarify this.