Thanks steven99,
It seems strange - seems to me the main point of selling SSLs through WHMCS would be to automate the process of renewal, validation and installation so you don't have certificates expiring accidentally.
The RapidSSL emails are "Your order is being processed" and "Order Complete". I'd assume these are automatically sent to the registrant email for the domain. Not a huge problem, just redundant when the cert is being automatically installed and we're sending order confirmations from WHMCS.