Thank you for clarifying this further Gutis. You explained it in detail.
What we basically need in a case where you have multiple certificates in the Certification Path of your real server certificate, is to have all those certificates Saved to one Cert File that CA SDM could use. Here's an example for smtp.gmail.com

So for SDM to identify the certificate for smtp.gmail.com, saving just that certificate (to base 64 format) is not enough. We need all the three certs, smtp.gmail.com, Google Internet Authorigy G2 and GeoTrust Global CA, all the three certificates "appended" together in one file. Order of the certificates does not matter.
To save each such certificate, you need to export each cert from the above cert to an individual file (in base 64format) and then append them together. For example, click on the Google Internet Authority certificate --> click View Details --> go to Details tab and then click Copy to File, Save it in base 64format to a different file. Repeat the same for GeoTrust Global CA certificate.

Now you need to append all the 3 files together into one, so it'll look like:
-----BEGIN CERTIFICATE-----
..
..blahblah Real SMTP Cert...
..
-----END CERTIFICATE-----
-----BEGIN CERTIFICATE-----
..
..blahblah cert chain cert1...
..
-----END CERTIFICATE-----
-----BEGIN CERTIFICATE-----
..
..blahblah cert chain cert2...
..
-----END CERTIFICATE-----
-----BEGIN CERTIFICATE-----
..
..blahblah ROOT CA cert ...
..
-----END CERTIFICATE-----
Save this file and use this file as the cert when configuring the mailbox.
Hope this helps
_R