TK, we appreciate the feedback and suggestions on how to improve our webmail interface. We often get requests for our webmail interface to be used on other mail servers or services. Unfortunately, this is not possible because protocols do not provide the functionality needed for all functionality available in the SmarterMail web interface. To achieve what we have everything is built on our API's.
We do provide functionality like continual mail imports for POP3 and IMAP and alternate SMPT as you referenced to allow some users use one interface for all their email, even if it is on a different mail server or service.
Regarding your request to save a message on another mailbox that was only used to send a message via SMTP, we have not encountered such a request before.