"Hmmph." Although Jin knew that Yun was merely a super enhanced NPC, that did not mean Yun did not have her original soul (despite pieces of it) within her. Jin figured that Yun was saying all of this, and doing all of this was ultimately for her son's sake.
She might not have lived long enough to sire the child from young to what -how Jin had become right now, but that did not mean she did not attempt or even try to do so. The realisation hit further as Jin rejected her when the System was still an asshole (maybe still is), but she continued to work hard for his store.
Whether it was because she had been programmed by the System to do so or it was her own willingness, actions spoke louder than words for she toiled for the store regardless of the reason. In fact, during his time alone in Atopia, his thoughts eventually wandered about Yun just not the extent that it would cause him to have sleepless nights.