You know... I said magical more as a sarcastic phrase. You see what I mean?
I wasn't even talking about the actual ability, and it gets rules lawyered.
Our group has finished Masks Of the Living God (a Pathfinder adventure) where they left Tamran, each of them with a mask and robe of Razmir.
They are going to - I assume - travel to The Looking Glass Deep disguised as followers of Razmir.
They are expected, and the first line of defense is a bunch of lvl 2 half orc rangers with favored enemy - human.
The party is 4 level and consists of 3 humans, an elf and a half orc.
How would you handle this when the defenders spots 5 humanoids wearing masks and robes of Razmir?
Asmo
Now that, my friend, is a doozy.
Well, I would say that a Ranger can identify creatures by other methods than merely sight. For instance, they might know how humans move that is different from other races. I would probably have the humans make disguise checks with bonuses granted by the clothing. If the orcs can see through the disguise, they get the bonus. If not, they don't!
Maybe something like this?
Now that, my friend, is a doozy.
Well, I would say that a Ranger can identify creatures by other methods than merely sight. For instance, they might know how humans move that is different from other races. I would probably have the humans make disguise checks with bonuses granted by the clothing. If the orcs can see through the disguise, they get the bonus. If not, they don't!
Maybe something like this?
Let's try a different approach - assume that the whole party is disguised as humans, because they don't want the elf and the half orc to be noticed. If the Orcs can't see through the disguises, do they get their bonuses against the Elf and the Half Orc because they believe them to be human, and thus their favoured enemy?
Does that mean I can cast an Alter Self on a dwarf so he looks like an Orc, and now the Ranger who has Orc as a favoured enemy gets his bonus, since he thinks he's fighting an Orc?
If tricking them into thinking the enemy isn't a FE when it is denies the bonus, presumably tricking them into thinking the enemy is a FE when it isn't should grant the bonus, right?
Does the need to actively identify a creature type go away if we instead think of favored enemy bonuses as due to something a Ranger's always doing? In other words, his fighting style is most heavily influenced by his favored enemies (bonus), but he doesn't specifically change tactics for them. Rather, he's developed a fighting style that's generally effective, but which he's discovered is especially effective against the opponents he's focused his hunting skills on?
That sort of thinking might carry over decently to the skill bonuses, too. He's not actively applying "I know elves think this way," to a Sense Motive roll, but the body language indicators he depends on happen to be those most prominent in elves.

(Dungeons & Dragons)
Rulebook featuring "high magic" options, including a host of new spells.