Disguise self is not a polymorph effect, unlike alter self, polymorph and anything based on them. It's an illusion, not a transmutation; it can't even have the Polymorph subschool because it's the wrong school for that. That's an obvious basis for understanding that it follows different rules.

The Disguise skill -- an attempt to "change your appearance" -- is what lumps together disguise self with alter self et al. Effects that change your actual shape also happen to change your appearance, which can be used to create a disguise, which is all the skill description is talking about. That doesn't mean effects which change your appearance also happen to change your actual shape. (I mean, do you really think your body vanishes from reality when you change its appearance with invisibility?) And it certainly doesn't mean all effects that can disguise your appearance necessarily reshape your body.

Thousand faces calls out the difference between an illusion and an actual physical change: it "is not an illusory effect, but a minor physical alteration". The text making that distinction would be unnecessary if disguise self was intended to change your body. Disguise self is referenced to describe the limitations of the reshaping, not to state that disguise self also reshapes your body.

And the point remains that disguise self leads to nonsensical results if you interpret "alter" (as used in the Disguise skill) to exclude the possibility of only altering how something looks. If one reading of the text leads to inane results and another reading makes sense, use the one that makes sense.