Note : @mezoology and I have been discussing this via email so that I could get some specific diagnostics. This is what I found out and emailed. I wanted to share it in case someone else has an OpenLiteSpeed server. Please be sure to make backups before editing or removing any files.
It appears that your web server is running OpenLiteSpeed. Newer versions of OLS don’t seem to rely on .htaccess except for redirects (maybe more but I am not an expert on OLS.) OLS also ignores .user.ini. The .htaccess limitations is why .user.ini was still visible after trying to hide it. But since OLS doesn’t care about .user.ini, you can just remove that.
To get the firewall optimized you have to do some additional configuration. To start you’ll need to remove the .user.ini file manually, like I mentioned above.
Then you’ll need to use the OpenLiteSpeed Web Admin interface to set the value for the auto_prepend_file.
This page tells more about using the php.ini override and how to use it:
https://openlitespeed.org/mediawiki/index.php/Overriding_php.ini_Values
The path you’ll need to add for the auto_prepend_file value is
/var/www/html/wordfence-waf.php
In reading more about OpenLiteSpeed, I’m not sure that newer versions even support .htaccess directives outside of rewrite rules and even then you need to restart lswl to get the server to read them (service lsws restart) so keep that in mind for adding things to it in the future.
So, if you do all that, you’ll clear the publicly visible file alerts for .user.ini since you deleted it and you’ll have optimized the firewall for the best possible protection of your site.
Thanks for your patience while I looked into this. If you have any follow up questions please feel free to ask.
Tim