First off, welcome to Team Chevelle Dwight!
Any legit Canadian-built 1969 Z-25-optioned SS396s, whether 300-Deluxe or Malibu based, should have come with the specific SS396 molding package (wheel opening moldings, rear cover moldings with black paint fill, deletion of other series-specific bright trim). They would not have used the Malibu script on the rear quarters.
I have seen an article on a Daytona Yellow '69 COPO that apparently came with the Malibu lower side trim & argent paint below that. I don't quite know what to say. Never say never, but it will take some real detective work and some solid proof to convince people of such an anomoly. I mean, assembly line workers didn't just decide to do stuff differently for one car
and expect to get it approved for release at the end of the production line. It would take a specific notice, bill of materials, authorizations to make it happen for a mass production assembly line at GM.
I'm with Don, skeptical but warily receptive (that is how you feel about it, right Don?

)
People regularly customized their cars back then. I remember back in 1968 a guy by my school (I was in grade 1 then) had a 1968 Impala Custom Coupe with the formal roofline like the Caprice. I distinctly remember the car having 1965/66 style Impala "Super Sport" emblems on the front fenders in place of the correct "Impala Custom" nameplates. Those things were attached by speed nuts and had to accessed from the inside.
Maybe the original owner of your '69 decided he wanted his Chevelle to be "a Malibu SS396". It may be as simple as that.