I fought hard to use the companion cert on a sleeper fare. I was more than willing to have the cert discount just the "Rail" portion of the ticket and not the upgrade charge but the 1-800 line said no can do.

I ended up booking 2 coach tickets on a long distance train, using the companion cert and then calling up to "upgrade" us to a sleeper. Was easy to do and only costed $300 (this was a NYC-MCO Ticket)