So, the issue seems to be that my notes have p-name, p-summary, and e-content, all set to the same thing (that being the full text of the note). Removing the p-summary solves the problem, and my notes display correctly in Indigenous. Thanks to Zegnat for the helpful explanation of how readers generally use these properties as part of post type discovery.
At HWC London tonight, looking into why the content of my notes appear twice in Indigenous Reader. Using pin13.net to check the microformats, and cross-checking it in Monocle (where it seems to appear correctly – content only included once.)
Heading off to Homebrew Website Club London shortly. . and posting about it from Indigenous on Android, to my website, which syndicates to Mastodon! Good times. #indieweb