I got Code to write me a better map into Apple Notes a while ago, as it wasn't able to see basic things like links, attachments, tables, etc. (I'm definitely no programmer).
Apple Notes in its current state is problematic to append to, although there a shortcut for that. Why? Because (to quote) "Note bodies live in ZICNOTEDATA as gzipped protobuf CRDT blobs." Wow, thanks Code.
However, with OS27, Apple Notes will be able to import/export Markdown. I asked Code if this might help. The answer is very likely yes, because the Markdown translation is also available in Apple Shortcuts. I'm kind of hopeful of being able to build a proper MCP in the near future.