Sorry but you are way overthinking.
My (lovely) ex mil made a similar joke re dd is the absolute spit of her dad but looks nothing like me at all! "Well we know who the dad is who's the mum!"
It's not meant critically it's just a comment on the phase he's going through.
My bro's eldest went through a phase of calling EVERYONE dada, many jokes made about this.
Best way to handle it would've been to come back at her with
"Who's X [one of her kids who looks nothing like her or dad]'s mum/dad it's a mystery!"
Or "well dh always has competition for my affections good thing I like him"
Or something similar.
You gotta toughen up and quicken your wit, geez you'd not last 5 mins with my lot!
I'm a ghost skinned redhead with piggy eyes among a family of near Arab looking (black curly hair, dark olive skin, dark brown almond shaped eyes) immediate family I've had jokes all my life about being adopted! (I'm the spit of one gran, seriously photos of us at same age are frequently mistaken one for the other - genes can be funny things)
I have to say given this example if maybe the reason you don't see "eye to eye" is you need to relax a little?
The only time I've known such a joke to fall flat in real life is when the paternity WAS in question! (Joke makers unaware of this).
And even aside from ALL that
If she meant it innocently shrugging it off as not meant maliciously is the right thing to do
And
If she didn't - then shrugging it off takes the wind right out her sails!