The gateway may also determine which client the payment is set to based on the payer email. Should that behavior no longer occur? If there exists another client account in the system, they could pay as one client and the payment could be applied to another.
The client ID is included when a payment is initiated by Blesta so that Blesta knows where to apply the PayPal payment regardless of email as it is included in the IPN call. The issue comes into play when data is imported into Blesta from a competitor and the client has a PayPal Subscription; in this case, client ID does not exist and a match on email is attempted, and the payment is not applied if a match cannot be found. This is a separate issue with a straightforward solution: Subscription ID's. PayPal provides a subscription ID for each subscription. We should really be storing this, and referencing the subscription ID rather than the email for such payments. I created CORE-2367 to deal with this.
Edit: To answer your question, we should not change the behavior if email match is only performed when client id is missing. This should never happen from a payment initiated within Blesta.
Is there a reason the payee email address is useful to know for a transaction? I think the PayPal reference field is currently blank and doesn't store anything like the last 4 of a CC number.