Scalix Connect for Outlook does indeed check the certificate's validity and signing CA, and have since the first release with SSL support. If I delete the root CA for my server's certificate, I get an error when Outlook connects to the mailbox, with a "Accept Once", "Accept permanently" and "Do not connect" dialog box. The client also properly parses intermediate certificate chains, as well as SubjectAltNames correctly. It uses the CA certificates stored in Windows in the latest release, a few of the earlier ones had its own way of storing CA certificates.
Are you sure you are connecting via SSL? By default if the client can access both ports it defaults to the unencrypted one.