Certainly would be available. You could order a 4 door sedan with a 427 if you wanted. I suspect a wagon too. As far as I know there were no restrictions on body style vs. engine.
I have seen a 66 Strato Chief 2 door sedan 396, so I don't see why a 4 dr ht couldn't have one. That sounds like a great cruiser!
You could easily document it with GM Canada.
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1966 Strato Chief 2 door, 427 4 speed, 45,000 original miles
1966 Grande Parisienne, 396 1 of 23 factory air cars (now converted to a "factory" 4 speed)