Went through 15-19 a few times, and I think it was more of a justification that "Archer is never supposed to be together with Rin, so don't worry about it too much", which makes sense, since if Rin were by Shirou's side the whole time, he shouldn't become Archer in the first place (this Archer also said to Rin at the end of UBW). However, it does make some sense to say that Archer (which more likely resulted from the Shirou from Fate route) could meet Saber again at the end of the journey, as depicted.