I run a 42" Recretec box in my 14' Trib. There is definitely a technique required to drop it into the bay. Well, drop is a generous term. Basically I do a little wiggle shimmy jive to get it most of the way in, then I have to lightly stomp on the center of the box to seat it. It makes me nervous every time to see those corners that close to the rubber, but so far so good except for a noticeable rub in one spot. I honestly don't know when or how that happened. My main concern is someone else trying to load it and causing damage to the boat because they don't know to hold their tongue just right.
As long as you don't trailer it with the box in place it would probably be fine, but honestly, if I had it to do again I'd go a little smaller. I think my suggestion is to err on the side of caution and go with the 38". You can use the money you save to buy rocket boxes or thirty packs of PBR to put in your Canyon.