You may as well be arguing that the type pyramid does not apply
Which it doesn't. It's ends up getting superceded for three entirely separate reasons (aside from being described as being more like guidelines than actual rules).
First, it's 3.0 material, and gets superceded by the template rules in the 3.5 core books.
Second, savage species isn't the primary source on this - the monster manual is, according to the errata.
Third, specific overrides general, and templates specifically stating that they change type from X to Y override the general case.
If people actually followed the type pyramid, then incarnate construct would inevitably result in a creature that was still a [construct].