I would ride that size, roughly, at 5ft 9. Though Canyon would put me on the next size down. It's equivalent to a 57-58 with a short top tube. You may be more flexible than me of course. I would have thought you'd be comfortably within their expected saddle height range. Despite being an endurance model, it's still a racy road bike and they will be sizing it for people to ride it with some drop from saddle to bar tops, just not Tour de France amounts drop, which may be fine for you.
Was the stem flipped up, or down, and how long was the longer one fitted?