The flat-footed when hidden bit is certainly a change, and a bad one at that. It's inelegant - generally, you are either flatfooted or you aren't, you aren't flat-footed against specific attacks or opponents. This raises way more questions that it answers. In particular, can you make AoO's (in general; I know that this isn't an issue with hide in particular)? This probably depends on whether you are flat-footed against an opponent or against an attack. Also, it is largely redundant with denial of dex to AC, since (if it doesn't deny AoO's), you already don't have dex to AC, so the rule is there for no apparent reason to include this. Actually, it does do something. It enables to ridiculous 9x cha mod to damage ability of the Iajutsu Master, but that's OK because no sane DM would allow the Master into their game to begin with.
Seriously, the last time they published a "flat-footed against specific attacks" ability (feat in RotW), the CO boards over at WotC turned it into another one-round kill almost anything build with, of course, the Master. The build was called the Killer Gnome II.
Tempest (of the WotC boards) helped make this build, and also helped write this book. I really don't think that he would intentionally put this in, but he could have noticed it.
That rule was way better in the core books.