Why? Who says you have to play a canon game? As you already concluded, any single game becomes non-canon as soon as you start playing.
Canon is for the (meta-)story side of D&D so that te various adventures, sourcebooks and novels can continuously build upon each other
For games canon is merely a jump off point
But, isn't that the point though? If every single game becomes non canon as soon as you start playing, what use is it to label the game canon or not? And, let's be honest here, most games are going to be non-canon before the game even starts. Players will want to play this or that class/race/background that is going to be not 100% kosher. DM's are going to add towns, NPC's, dungeons, events and various other details before the first die is dropped.
Doesn't that make the notion that a campaign is canon or not a pretty nebulous idea? At best, you could be close to canon or far from canon, but, virtually from word go, you are going to be straying from canon. And, if that's true, what's the point of telling someone else that their campaign is canon or not?
And, as far as the meta-story side of D&D building upon each other, let's be honest, that's a house of cards at best. The canon of the game has changed, and sometimes changed radically over the years. How solid of a foundation are we really working with here? Whether you want to talk about core or specific settings, what is canon is a high speed moving target. What is a _____ is a question that depends on who's asking and when.
Again, I have no real issue with the idea of canon/flavor as a starting point. Fantastic. It's something to use to generate ideas or get the creative juices going. No problems. And, if that was as far as things went, I'd shut my mouth and not worry about it. For example, there's a thread on the boards right now:
http://www.enworld.org/forum/showthread.php?522355-Seeking-details-for-5e-Neverwinter-beyond-SCAG about someone looking for a bit more details about Neverwinter for his/her campaign. Ok, cool. No problems. I can't help, as I'm not really up on the material, but, fair enough.
My beef comes when changes get judged based on how well they dovetail with what came before. That's my bugaboo. The idea that a concept is bad, not because the idea itself is bad but because canon has some sort of intrinsic value that means that what came before is automatically priveleged. It baffles me, mostly because it gets applied so unevenly. It's perfectly acceptable, for example, to make succubus not demons or devils at all, but, changing them from demon to devil was completely wrong? Bwuh? If canon has intrinsic value, then these changes should be judged accordingly.
But, like I said, the judgement is based far more on the preferences of the judge than on whether or not something really is a change.