There is no relation between ARQ and the Plugin Firewall. They are 2 completely separate / different security features. The Plugin Firewall is designed to protect the “plugins” folder so that ARQ does not need to check/monitor the “plugins” folder/files.
If you are excluding the “plugins” folder in ARQ then the plugins .htaccess file will not be backed up because the ARQ Exclude rule says to not backup any folders or files in the “plugins” folder, which includes the Plugin Firewall .htaccess file.