Thought experiment: (just using companies I think HN will be familiar with, I'm not involved with these.)
1. You're Tumblr or Basecamp or Slack with thousands/millions of user.example.com user subdomains
2. You want to protect all of them with a root HPKP policy with includeSubdomains, because users will be bouncing between them, and with that many trust-on-first-use gaps, it'd be pointless otherwise.
3. And then you want status.example.com hosted at StatusPage, blog.example.com hosted at Medium, and someapp.example.com hosted via GitHub Pages with a CNAME. Assume there are long-lived links to all of these subdomain URLs.
You can even assume that the third parties implement HPKP, and that they'll never have a hiccup.
There's no way to make this work without either:
A) Removing includeSubdomains, and no longer catch a large amount of cases as users traverse your site, barely solving a problem anymore
B) Serving a concatenation of every third party pin, opening up gaps huge enough where suddenly every CA is now authorized again, not solving a problem at all.
C) Noticing something I haven't.
And note that there are security (not merely vanity) reasons for using subdomains instead of paths for hosting user-generated content. I don't think this is too crazy of a scenario.