The polymorph subschool rule regarding HP does not apply to the regular polymorph spell since there is actual text, in the spell, that claims you assume the physical stats of the creature and replace them with your own. Ergo, your HP changes as a result.
Assuming the physical ability scores of the creature without changing hp is the way polymorph subschool spells work by default. Thus changing physical ability scores without changing hp would, unless contradicted by the existing rules text, be the way polymorph should work. How does changing physical ability scores contradict changing physical ability scores without changing hp? There is after all precedent for changing physical ability scores without changing hp, so changing physical ability scores does not necessarily in itself imply changing hp. The existing rules text for polymorph never mentions anything about changing hp either way.
For the purpose of adjudicating effects that apply to polymorph spells, any spell whose effect is based on either alter self or polymorph should be considered to have the polymorph subschool. However, note that the spells' existing rules text takes priority over that of the subschool.
Read the section on "spells that came before". It specifically says that the polymorph subschool stuff doesn't apply to Polymorph, Alter Self, Shapechange, and other "spells that came before" at all.
The passage you quoted me quoting is from that very section. And as you can see it doesn't apply if the existing rules text states something different, which is not quite the same as "at all".
For the purpose of adjudicating effects that apply to polymorph spells, any spell whose effect is based on either alter self or polymorph should be considered to have the polymorph subschool. However, note that the spells' existing rules text takes priority over that of the subschool.
Polymorph is based on alter self, and thus belongs to the subschool.
Shapechange is based on polymorph, and thus belongs to the subschool.
Alter self is mentioned as an example of how the new rules affect existing spells of the subschool, and is thus obviously intended to belong to the subschool by the designers.