Master of Many forms and Human Bonus feat

[Gruftzwerg]

While feats default to (Ex), that's not necessarily true of the abilities that grant them. The human's ability to select an additional feat is a natural ability, not an extraordinary ability, even though the feat itself is most likely (Ex). Also, it applies at 1st level during character creation, so you can't necessarily gain it from a shapeshifting effect. Furthermore, bonus feats in general are not considered special qualities (they have their own, separate line in statblocks), so it doesn't actually matter that they're (Ex). And finally, alternate form says the creature retains its own feats—it doesn't gain the feats of the new form.

I don't think that they default to natural abilities because:

Natural Abilities

This category includes abilities a creature has because of its physical nature. Natural abilities are those not otherwise designated as extraordinary, supernatural, or spell-like.

While the second sentence defaults everything unlabeled to NA, the first ability excludes mental abilities. And HBF is a mental "fast learning" ability.
IMHO the sole category that makes sense (for HBF) would be EX. It ain't a spell/like ability nor a magical supernatural ability, which leaves EX as sole option.

And my last argument would be "text trumps table". As long as the there is text that supports that HBF has to be a extraordinary special quality the table is irrelevant. We have seen enough dysfunctional tables in 3.5 so far. Just because the tables don't reflect the extraordinary special quality source anymore doesn't change the source of that ability.


edit: I don't think the 1st lvl restriction for HBF is a problem here. We can assume that Wild Shape transforms you into a 1st lvl equivalent of the target creature type by default if it doesn't have a fix HD. In chase of humans that would be a "commoner 1". You have to keep in mind that wild shape forms represent just matured fresh out of the box versions (referring to stats! not visually!) of the desired form.