Issues with Security & Setup warnings

php 7.3.15 (php-fpm cpanel)
Apache 2.4.41

Three issues

  1. I understand the point of security checking the integrity of core files, but why is it necessary to report other files in the site root folder as security issues. I have NC in the public_html folder not in a sub-folder (it is on a subdomain), and the system puts a php.ini and user.ini there which the security check reports in red as having not passed the integrity check. In the case of user.ini it is now reporting it as having failed the hash - which is nonsense. Can I not have a whitelist of allowed additional files, and files to exclude which I can edit? Or better still have the option to turn the security check off? Suppose I want to hack around with core files - I might want to do that and be able to exclude those from the security check.

  2. It is reporting that OPcache is not properly configured despite the quoted commands being included in the (cpanel-edited) php.ini in the site root folder.

  3. In the log I am getting 4 instances (with different line numbers) of the following error every few seconds

shell_exec() has been disabled for security reasons at 

does this matter, and what is causing it - everything seems to be working normally.