The problem was not in my redirects, but instead it is a bug/lack of a feature in the existing AMP for WP plugin. The issue is described here and the bug fixes are shown here if you want to be brave and patch the plugin directly. I can vouch that this works for my root directory issue for the current 0.9.58.1 release.
If you don’t feel brave, as far as I can gather from the GitHub page, this fix should appear in version 0.9.59, which might be in a couple of weeks or so.