I don't believe that canonicalization and redirects are the only reason for supplemental results. Most of my site went supplemental long AFTER I did a 301. Some 10 months later.
Ask this engineer if pages can be pushed into supplemental because of lack of inbound links. I'm not talking about from the same base href but outside inbound links. I am highly suspicious that there has been a trend since Big Daddy to send pages into the supplemental if they have none. If so, can they ever be restored to the regular index.