Continuing the discussion from Can I define a custom source or folder from which my site hosted on GitHub pages can load from?:

Not sure what your question/message here is… Could you elaborate a bit further?
If you want a PR template, then make a PULL_REQUEST_TEMPLATE.md file inside the .github directory itself (Not .github/ISSUE_TEMPLATE. This won’t work).

You could also have multiple issue templates stored in a PULL_REQUEST_TEMPLATE folder, but unfortunately does GitHub not offer a PR-template chooser similar to that of issues itself yet, which is quite a downside.