Pet Mods don't work in Operator Mode and Operator doesn't earn affinity directly.

[(XBOX)DarkPhoenixRise]

To Reproduce, equip a pet like a MOA then run a lowish level mission, like teshihub in void. Exit Warframe at the beginning and complete the level as the operator only. Animal Instinct and Vacuum will never be used by the MOA despite being right next to  you.

 

Nothing showing up on mini map despite presence of pet.

Crate not showing up on mini map despite pet being right there

Vacuum not working despite pet being right there.

Mission Complete screen, you can see the Pet got plenty of affinity, but the operator got none towards the school they were playing.

 

Just to show that the pet was actually participating, reviving the pet.

 

Pet Build