if you love Free!, first of all, you should read this Final Stroke staff report no matter what: https://fs.iwatobi-sc.com/special/second_greeting05/

but if you love rinai specifically, you should scroll to this section here:

after watching fs2 a few times i asked myself, "why is ai in this scene at the very end when it'd make more sense for rin to have sousuke present, given the final relay?". i could posit that maybe it's because ai had been there from the very start (of the series, not of the timeline). after reading the staff report, that much was confirmed!

my translation skills are pretty rudimentary, but the tl;dr here is, the very same director who worked very closely on season 1 was responsible for this scene in fs2. kawanami-san remembers working on a Free! that didn't project itself beyond season 1, and as a result, the image of rin and ai together as a "set" is fresh in mind. because they wanted to invoke a "tied-ends" feeling to these series of scenes at the end of fs2, they chose to put ai with rin together in budapest.

the actual sentence there is (to the best of my knowledge), "the first season had these pairings* - haru and makoto, and rin and nitori - and i'm building the story around the image of coming to that conclusion."

*the specific word used is 組み合わせ or "kumiawase" which translates roughly to like, "a set piece/a set pair/a combo", which i think is very cute. even without ship goggles, it feels very much like coming home, seeing the very end set up in such a way. fresh off a season 1 rewatch, the two of them certainly are shown together a lot, and i'm looking forward to reaching fs2 in my rewatch with all the material fresh in mind.