First, when "Marry Me A Little" was partly written (not even completed) as the last number, Amy did not get married to Paul in act one. Robert came to her late in act two and proposed with that song. I am sure more followed, but I don't know what. I think Amy probably rejected the proposal. Sondheim did not complete it at first either because it was clearly not right (he told it that way once) or because it was decided before he finished it that Robert would not propose to Amy late in act two. I think he told it that way, or someone did, much later. He completed it as a present for Judy Prince, because she had so liked what he had written of the song. Sondheim got Harry Nilsson to record it, and Sondheim gave it to Judy Prince as a present.
Second, when "Happily Ever After" was the last song, it was followed by a scene where Robert, having not gone to his birthday party, goes to a park where he meets a new group of people, including a woman with whom it seems he might become romantically involved.