This is the expected behavior when logging using a domain alias. The other aliases won't be available since the user has specified an alias during login. An alternative solution: Have the user log in with their corporate domain. In Account Settings, they can set the "Default From Address" to the domain alias. All replies and new messages will be sent from that domain alias address, and they can manually change the Send From dropdown as needed.
Another useful setting they could enable is "Use To: address to replies". When enabled, replying to a message via webmail will use that email's To: field as the Send From address of the reply, regardless of whether the message was sent to their SmarterMail email address or a domain alias, email alias, SMTP account, disposable address or plus address. For example, if an email is sent to the user's corporate domain, their reply would come from that same domain address. This setting does not prevent the user from manually changing the Send From address when composing a message, so they can adjust the From address as needed.
I hope this helps!