The plugin currently has a is_alternate_wp_cron() function to check for the ALTERNATE_WP_CRON constant, but it is only used to output in the debug information. When we have the alternative cron enabled, we still receive the "Cron not running" email.
Would be great to have a is_alternate_wp_cron() check within the maybe_send_cron_error_email() function that would cause the email to not send.
Currently the only fix is to just disable the email completely by using the wposes_send_cron_error_email hook.