Email Parsing Engine Stripping Code

We have created custom email notification templates by duplicating the core templates into the child theme as per the docs. The HTML of the emails has been tested outside of the WooCommerce ecosystem and work fine.

Once they are placed into the email-header.php, email-footer.php, email-styles.php and customer-invoice.php format certain pieces of code are stripped when the emails are produced out of WooCommerce.

This is code being stripped:
https://gist.github.com/anonymous/aaaf9bb73eaabff0bc9976f2d72ff6cf
https://gist.github.com/anonymous/ee81354ac4d731234a5a569fb623ae7f

This code allows us to do custom content on desktop and mobile and we need a fix to stop WooCommerce stripping it.

Any suggestions would be greatly appreciated.