There is a conflict with the WooCommerce SimplePay Payment Gateway plugin. It calls WC()->mailer() before the theme registers its own emails, which is why the waitlist emails do not appear in the WooCommerce Emails list — https://gyazo.com/4f4606d1244c718e0897e21a08f38095
This can be seen in WooCommerce → Settings → Emails.
If the plugin is disabled, the emails are registered correctly — https://gyazo.com/b4b051271ea3f8013324f6482a95acb5
This issue is caused specifically by the plugin, because the same conflict occurs with other plugins that add their own WooCommerce emails. You can verify this using the YITH WooCommerce Waitlist plugin, which also adds its own emails — https://gyazo.com/b76689ac352054abd4dff3a5036ffa52
When WooCommerce SimplePay Payment Gateway is enabled, these emails are also missing.
The issue originates in the following file:
wp-content/plugins/wps-woocommerce-simplepay-payment-gateway/includes/WC_Gateway_SimplePay_WPS.php
specifically at this line:
$mailer = WC()->mailer();
.
