Batou literally thought of his Tachikoma as his child.
In the 16th episode of the first season, he's shown looking on as the 'komas are lead off to the lab but they're never outright mentioned again in the episode. Midway through the episode we get to see a faked photo of his cover identity's wife and kid (who looks an awful lot like Motoko). At the end of the episode he smashed both the bottle of liquor that was given to him "for his wife" and the bottles of all-natural oil that he previously gave to his personal Tachikoma. Taking into account his crush on the Major...2nd GIG does not give us Motoko's backstory.
While it's never explicitly pointed out, several previous episodes in the Stand Alone Complex continuity seem to note that Motoko has a natural gift for filling vacant roles in somebody else's narrative, even when she's not looking for one. While the girl described in AFFECTION certainly has a past compatible with what we know happened to Motoko, most of the evidence it really is her consists merely of Motoko never denying it. And when handed the chance to become the arguably most important person in the life of her current mission's main target - she wouldn't deny it.