How could you possibly give him the upper hand against Canelo and Cotto? You talk about them having to train for something they've never seen, but Conor would be in the ring against technical skills he's never seen, nor had to deal with. Ever. These are elite boxers, the best of the best, which Conor has never had to fight in a boxing ring. It's easier for the elite professional boxers to deal with an amateur unorthodox style than the amateur having to deal with the elite pro.
You mentioned that training for boxers is simpler because it's just small subtle differences between them. Which I don't think is true first off, try training for Floyd and then a guy like Maidana. It's such a different type of fight. But still, those small subtle differences you mention are simply because punching is the only weapon. Conor himself has to abide by that, so whatever amazing flowing movement he has, in the end he's still going to have to do exactly the same thing as his opponent - throw punches. So it becomes then, who is the better skilled throwing punching guy (also known as "boxing").
I think it will really show tomorrow if Floyd wants to embarrass him. If he just stands in the pocket the entire time, which he says he's going to do, he'll get a KO but he'll probably also make Conor look competent for a couple rounds simply due to Floyd making himself more available if nothing else, which Floyd has done a lot more in his advanced age. But if Floyd really wants to put on a number and embarrass him, he'll use movement as well.
Guys like Canelo and Cotto are so unbelievably technically sound, that they can exploit simple things like having a bad stance, leading with the wrong foot, over extending, missing a power shot, etc., they can punish his body and head. It wouldn't be pretty in either situation.
If Conor wants to use a wide karate stance, it's not as if boxers have never seen a wide sideways stance before and will self destruct because they won't know what to do. Some guys in boxing use very wide stances, some have different backgrounds in kickboxing or whatever and some guys are just weird and unorthodox as fuck. These guys like Cotto all go through years of amateur boxing on the international level and see it all, on the highest levels, and learn how to handle it and weaknesses they can exploit. Of course Conor can do some movements that are different, but in Boxing it still boils down to throwing punches and timing. It won't take much to see what Conor is made of and he'll realize rather sooner or later that timing in boxing against an elite boxer, when punches are the only weapons you have, is completely different than in MMA which is just so different for a number of reasons.
I don't think it gives nearly enough credit to guys like Cotto and Canelo, who are incredibly skilled boxers, to give the upper hand to a guy who you've never seen box professionally before, or to the sport to suggest they wouldn't have the upperhand, simply because Conor "is a fighter" and will do things "they've never seen before" (which you haven't even seen yourself either).