The
Emissary Familiar Archetype on the Archives of Nethys matches what you say you're seeing on your familiar, replacing the proper abilities. It's also what I'm seeing on a test character.
The
Chosen One Paladin Archetype describes the other abilities you're saying are missing from your familiar. They're applied to the Paladin, as you can see under Special Abilities on the Paladin tab for your main character.
Unfortunately, that means you'll want to use Adjustments to fix the familiar's Knowledge (Religion) and (at level 11+) give it the Smite bonuses, if you want it to go into combat. At level 7 you'll have to change your familiar's "race" manually, just like when you take Improved Familiar. The
Change Shape universal monster ability that lets it go back to its original form doesn't change your familiar's stats, which should help if you need a full combat character sheet for its original form after getting True Form.
If you haven't already, you could submit a
bug report via the website for the abilities that are given to the Paladin but apply to the familiar; even if they can't be added automatically maybe LWD could add an Adjustment for them. They haven't been doing much work on PF1, though.
Hope this helps.