Regarding the little sister. I don't recall if they ever spell out what happened to Tomo's mother, but if she's alive and just left when Tomo was, say ten years old, then it's entirely possible that the epilogue takes place about ten years later, as the little sister is most likely from the mother's side. No way that Ai could be over 40 and still look almost identical to when she was in university.
As someone with two younger half-siblings who I share a mother with, I can tell you that yes, it's entirely possible for maternal half-siblings to look uncannily similar. It's actually a bit of a myth that people get most of their looks from their father. Hell, I have more physical traits in common with both my younger siblings than they have with each other, and they have both the same dad AND mom.