To accomodate a complex layout like this, webmention.io-backup would have to parse the config file and look up the date field in all the content files’ front matter to figure out which directory corresponds to which website page (basically, the way Hugo does it when it creates the pages in the first place). Programming all this is not impossible, of course, but it would be quite an endeavor that I’m not sure I want to embark on, especially considering the fact that one’s config.toml may contain something along the lines of

[frontmatter]
  date = [':git', 'lastmod']

I don’t want to open that can of worms!

These ‘mentions’ on my side aren’t being threaded back to the original post.

Beware, this is Salmention territory you’re stepping into. There be dragons.