Hello. I got the same issue as OP.
WP directory is site.com/wordpress, but the page shows on site.com
When Coming Soon is enabled, I have to go to site.com/wordpress to see it, otherwise I get the Coming Soon message.
Same thing for posts and comments. I have to go to site.com/wordpress/?p=1 to see it working. If I omit the “/wordpress” part I get the CS message.
I followed the steps linked above to move the installation.
Thanks ??