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This makes sense since moving the Crons folder rests outside of the public_html directory and Single 5.4 php is set for the site.
All of the crons set-up need, in my case, the extra bits " -c /home/username/public_html/php.ini" to work.
The automation and domain sync now work after doing this.
Some scripts executed with a Cron Job requires a specific php.ini file to be used.
When executing a PHP script from a Cron Job (or via the command line), you can use a custom php.ini file. The most common situation where a custom php.ini file is needed is when a user's code requires access to something such as Zend Optimizer, which is specified in the php.ini file.
Specifying the php.ini File
To specify an alternate php.ini file, you'll need to use the -c flag in your PHP command line.
For example:
php -c /home/username/public_html/php.ini /home/username/crons/domainsync.php
In this instance, /home/username/public_html/php.ini is the full path to the php.ini file you'd like to use and /home/username/public_html/myscript.php is the full path to the php script you'd like to run. Using your actual username, change the path to the php.ini and the file you intend to run accordingly
Note: Your home directory may be home1, home2, home3, etc.