There was a major 'Series finale' vibe in the last episode of season 3. It brought the main themes of the show to a head and even ended with an expanded version of the song in the opening credits. It even glibly summed up all of the show's messages: "Doing things for other people is good. Doing things for just yourself is bad." Dan Harmon clearly intended for the show to be able to end on that episode.
You're ignoring the context of that time. Harmon was already exiting the program and a season four renewal was not certain yet when production wrapped in mid-February 2012. Likely, he decided to close up as many threads as he could in case it was the end, but still leave room for the show to continue if it did get that season fou renewal. Which it did, three months later in May, 2012.