Partner Seal only check your base class, since Takumi has different base class than Oboro, he will get any class from Oboro's base class, in this case Spear Fighter even though he already has it as his secondary class. Some rare case example is Takumi x Mozu. Because Mozu can't pass Villager to Takumi, the game made her secondary class (Archer) as base class for her buddy/spouse, and because Takumi already has archer as his base class then he will get Villager hidden class which is Apothecary.