It's worth noting the Yuri Natsu Afterstory short was originally written around the time of Wagayuri volume three, so what was included then may or may not impact the story now. As for Yoh and Miki, Hana poking her after the dodgeball tournament seemed to me to indicate that they're still very close, at the end of Yuri Natsu Miki had a pretty solid plan for what going to the mainland would look like:
https://mangadex.org/chapter/f49ba713-4353-4590-8838-e8a10ea6f41d/3
She said then that she would try it out for two years and if she wasn't making progress as an artist she would come back to the island and get a "real job" to support Yoh and the Inn (the same way Yuu works as a fisher to provide for Nene and their families). It's been two years now, so I suppose we'll find out soon if Miki is coming home or staying on the mainland with Tsubomi!