Ah, that's too bad.
I'd love it if "Skilled" just added trained to the Familiar. And if it either scaled with level or allowed you to take the ability multiple times in the same skill raise its proficiency level at appropriate times.
Or the first "Skilled" for Trained, and the second "Skilled" for scaling. Considering how you'd likely need Manual Dexterity, Independent, and some communication form as a minimum.
It would allow familiar skills to be useful into the late game and give familiar holders another meaningful choice to make to fill gaps in the party.