[3.5e] How does the Disguise skill work?

[Gale]

One of the players in my campaign is planning on disguising her female character as male. Thus I looked up the Disguise skill in the Player's Handbook and I noticed it doesn't clarify what actually happens when someone succeeds on a Spot check against a disguise. The obvious implication is the spotter notices the person is wearing a disguise. But how detailed is this realization? Does it allow someone to see their true identity, in this case that they are actually female, or is it limited to simply noticing the disguise itself?
Also, how does Alter Self work in regards to the Disguise skill. I know it grants a +10 bonus to Disguise checks. But if someone uses it take a new identity then why should anyone be given an opportunity to make a Spot check against them? It makes sense when someone attempts to use Alter Self to pretend to be a known individual like a king. But in an instance where perhaps a human uses it to take the form of a random elf why would anyone find them even remotely suspicious enough to warrant a Spot check? Even if they succeed what exactly are they noticing anyways? The human in disguise as an elf does actually have the form of an elf in every sense. How do you spot something that essentially isn't there?

[DeltaEmil]

If those who make the Spot check win, they simply figure that the person is wearing a disguise. Nothing more. What they do with that knowledge is up to them. The human that disguises as an elf would not be recognized immediately as a human if the spotters do not check for it, but they know that the "elf" is somehow disguised or using a disguise.

As for using spells like alter self, polymorph, and disguise self, as long as the disguised person does nothing that would draw the attention of the watchers, the watchers do not make Spot checks, as per the Disguise skill.

So, if a harmless human wizard simply polymorphed himself into a random elf, people that do not care about the disguised person will not attempt to see through the disguise. Guards on active duty looking for troublemakers and spies are allowed to make a Spot check to see if that random elf is somehow behaving unelvish (clumsier movements, too much muscles, does not cough all the time). Soap makers just selling their soaps to that random elf do not get to make a Spot check.

[Extra Anchovies]

Guards on active duty looking for troublemakers and spies are allowed to make a Spot check to see if that random elf is somehow behaving unelvish (clumsier movements, too much muscles, does not cough all the time).

I love you. Thanks for the laugh, I am much better for it.