>>31948561) I think they just picked their favorite chapters (or the ones they thought would make the best anime), or that's the theory you often hear. Especially season 1 mixes a bunch of things from different chapters together, so they probably weren't expecting to do more than a single season. The chart that floating around makes it seem like the episodes neatly match with specific chapters, but that's not really true with season 1.
2) The earlier parts of the manga are out of order too, since Ume was just drawing chapters that matched with the real life seasons, so you'd get a Christmas chapter around Christmas... even though you in the previous year you had a New Year's Eve chapter, without the (school) year ever changing in-universe. So it didn't make much difference if they jumped around a lot in the anime too.
I think 1) makes more sense. I like an adaptation like that more than the kinds of adaptations you mostly get, where they're just following the manga without even trying to do anything interesting with it. It makes reading the source material after watching the anime more fun too, since you're not 100% familiar with the first few volumes already.