I’m just testing pinegrow out, so definitely not an expert, but I’m fairly sure this is a bug.
When working on a Wordpress theme, if there’s any other page named “index.html” inside a subfolder somewhere, then that file is used instead of the actual master when I select “Wordpress -> apply master page”. If I remove or rename that index file then things work as expected.
Pinegrow 5.95
macOS 10.15.4