I could see changing it if they decide that proficiency increases no longer function as the feat/feature slot.
Weapon proficiencies don't count as class feats for weapon classes, so I don't see why spell proficiencies should for spell classes. It's also a massive pain for "mystic theurge" type builds who want to get a class feat at precisely that level.
The book states that Specifics override general rules, thus the Feat does in fact override the no Heritage Feats beyond level one rule.
Ancestral Paragon let's you gain a level-1 ancestry feat. It does not, however, allow you to gain a level-1 ancestry feat for which you do not meet the prerequisites. Heritage feats have the prerequisite that they are taken at (character) level 1. If Ancestral Paragon overwrote that, then it would also allow you to take a level-1 ancestry feat from another ancestry.
I seriously cannot understand why metamagic feats are not general feats anymore. Metamagic should not be class specific, return metamagic to general feats.
Because they fit the design space that Paizo wants class feats to fill, not general feats. They aren't all that class specific, either. Multiple metamagic feats are shared across several classes.