When I do my SAS 9.4 server install I break it into phases:
1) install-only (no deploy) to get a populated sashome
2) add my custom CA certs (intermediate and root) to SAS Trusted CA Bundle - see Manage Certificates in the Trusted CA Bundle Using the SAS Deployment Manager
3) deploy-only to get populated Lev1
If you have an EV cert from a well known CA then I imagine you will have skipped 2 (or only added the intermediate) and perhaps combined 1 & 3 into a single step.
Looking at my recorded deployment response file, I can only see the server cert specified and looking at my notes I don't see any references to SSLCertificateChainFile, however based on the name of the file I highly suspect it was a manual post-deployment change to the Apache config by me - along the lines of Updating the Key and Certificate That Are Used by SAS Web Server but with a SSLCertificateChainFile that contains the PEM encoded intermediate and root certs.
From memory, with the SAS Deployment Wizard Typical level of prompting, you get to specify the server cert and key files (but not chain file).
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