How ApisCP is different to Cpanel

Cpanel tends to run everything as the user, which makes it very easy to overwrite files by a hostile script exploiting a issue with wordpress

ApisCP runs php as a different user, leaveraging cgroups and group permissions to control how things can be modified on the website.

In order to upgrade modules, the site needs to have foritication modes changed to allow the writes you require. You can also have custom profiles to allow certain writes whitelisted.

You can use Learning Mode under Fortification to give it the least permissible set of write privileges

You can also go the opposite direction and have PHP behave like cPanel by going to Web > PHP Pools and changing the owner to your account admin. This will allow PHP to write to any file in your directory the same as Cpanel does. The downside being the removal of the security protections.