Version 7.0 fixed this issue.
Thank you!
Might it be a better solution to fix the plugin issue then try to solve this per server configuration? It seems from reading other issues, there are a few others with the same root issue.
Other apps have this working fine such as Yoast. Maybe review how they have it programed to determining absolute root vs WP installed location? Or add an option in the plugin to set the root folder / subfolder of the WP installation?