Could be they check if an item\xe2\x80\x99s content starts with its title, and decide to display it as a note if so (this is how, again, popular PHP library X-Ray does it). One way to have both notes and checkins not look like articles is to remove their title tags from your RSS (and not use a p-name in your HTML, but I believe that is already the case) altogether. That, in my experience, is the trick (and perfectly valid).
@help Do you ideas why my checkin status posts display photos inline on micro.blog fine, but my checkin posts appear like articles? RSS Feed html is the same, but microformats are different on the post itself (status vs checkin) – is micro.blog fetching / parsing that to decide how to display content on the website?