Issue with URL rewrite resolved
It appears this had nothing to do with MySQL / MySQLi - initailly I thought it did because we were using an include file to set the path of the website in the urls.... My error had nothing to do with the url path either.
In WHM -> Service Configuration -> Apache Configuration -> Global Configuration, "Optimize .htaccess (AllowOverride)" was set to "Search “Home Directory” and below (Recommended)". Setting this value to "Search “/” and below (No optimization, Search Full Path)" made your site load as expected.