I was doing that for debugging purposes because of what the guy had done in that thread you linked, Broken Theme Directory
So I followed what Foxaii was saying,
I haven’t been able to replicate this and have managed a Bedrock install at both localhost/wordpress/ and localhost/wordpress/dev without any issues.
I would guess that the WP_CONTENT_DIR is being set incorrectly, which is defined here. Also note where the $root_dir variable is set near the top.
If you troubleshoot some of those defines we may have something more to go on.
I output the $roots_dir in /config/application.php and got /var/www/payroll, and then it appends /app starting at line 25? So that is right… right?