From my understanding, it is partly a Jerboa issue.
For the !community@instances links, I believe the links are being parsed automatically, and are getting set as email addresses. Jerboa should be able to recognize those as links to Lemmy as handle them correctly.
For the instance/c/community links, Jerboa isn’t really able to detect whether it is a Lemmy instance or just any other website, so they have predefined a few instances to be handled by the app. This is what people are talking about with Android being dumb. You should be able to set custom links (i.e. any Lemmy instance, not just the ones set by Jerboa) to be opened by default by Jerboa, but Android doesn’t allow that.
Comments are sorted by “Hot”. Jerboa does not specify a specific sort order it wants, so Lemmy gives it the default, which is Hot.
https://github.com/LemmyNet/lemmy/blob/ecc9469a02e63eab4e19093007c7ba6db0dca079/crates/db_views/src/comment_view.rs#L348
https://github.com/dessalines/jerboa/blob/1687634f4441d92dcd7a24f500aa07b25ef270d2/app/src/main/java/com/jerboa/ui/components/post/PostViewModel.kt#L89