I've built a very minimal, plain site using pkgdown, and while it works great locally, the links seem to break on Github. This issue has been previously discussed here:
though not clear what @ajpelu's solution was. My site broken link is here:
Solving my own problem here, but keeping it up for others that may run into the same issue. This was dumb - but I realized I had added some of the docs/ folder to the .gitignore, and thus that was causing the problem. So with the right files, pkgdowns' links work great!