Use WP Encrypt with Domain Mapping

I am using WP Encrypt to generate and install SSL certificates from Let's Encrypt. The issue is that the mapped domains (I use subdomains) are not being picked up by WP Encrypt. Apparently WP Encrypt looks for the domain to add to the certificate from the Site URL field. I guess domain mapping doesn't change that field, but leaves it as a subdomain. I tested this by changing the Site URL on one of my mapped sites to see if it would pick it up and it did.

So my question is, is there someway to add a filter or something so that Domain Mapping's virtual domain are picked up by WP Encrypt. The process of generating and maintaining new ssl certificates is so much easier with this plugin, but it does me no good if the mapped domains aren't picked up. The developer of WP Encrypt said that this filter would pick it up, but it doesn't:

/**
* Filters the addon domains to create the certificate for.
*
* Using this filter basically allows to generate the certificate for any URLs,
* even those outside of the WordPress installation.
*
* @since 1.0.0
*
* param array $addon_domains The addon domains.
* param string $domain The root domain for the certificate.
* param bool $network_wide Whether this certificate is created for an entire network.
*/
$addon_domains = apply_filters( 'wpenc_addon_domains', $addon_domains, $domain, $network_wide );`

From: https://wordpress.org/support/topic/multisite-with-domain-mapping-problem/

Would there be some way to use this: https://premium.wpmudev.org/forums/topic/get-domain-mapped-url-from-all-my-sites#post-936438 to create a parameter to add to this filter?

Thanks!