Thank you for the extensive amount of info about the situation here in Canada. Good to know

. Though my account appeared to be registered in Canada, I literally just came to Ontario for a couple of days. So there's a lot to learn.
You are right. For someone (including me) who seriously considering getting an APR tune, they should definitely contact VW Canada and APR officially and get answers. Or just willing to take the risk and accept whatever the repair APR warranty can offer, or worst case, pay for repair for it themselves.
Me stating some info about APR was only out of my personal interest, NOT to encourage average owner all go and do it.
About the car:
Also, I understand that majority of the owners are kind of scared when they heard something could "void the warranty of xxx". The fact is that a major drivetrain part will not break, within the warranty period, w/ or w/o the tune, in most cases. (marketing scam or not, this is literally most of the cases)
Each major components on the vehicle is designed with a certain amount of headroom for stress endurance. For example, your stock engine output is 500hp, the engineering headroom for the engine is 20%, you can raise the power output to 600hp and theoretically not cause any damage to the drivetrain. (In some cases, trans, diff, driveshaft and half-shaft can withstand more stress than the engine parts, thus maybe rated to 650hp)
Since EA888 and the MQB platform is shared by multiple vehicles, the rated specs are not that hard to find.
If you tune it:
Surely, tuning the car for more power will reduce the lifespan of the parts involved, but it takes a very long time for the affect to show some symptoms. By then, you are most likely to be out of factory warranty, w/ or w/o tune, you have to pay for the repair.
But we are only talking about a stage 1 tune here, not some extreme 600HP mod. APR is a large company who did stability test of their tune prior the release. So critical issues like a blown engine, turbo, trans, transfer case, or even a shaft caused by the tune is very unlikely, unless you track the car, tow heavy weight, or bashing the car off-road, on a very frequent basis (problems can also happen even if you're bone-stock b/c the stress is much higher under these extreme using conditions, or at best, extra wear of some parts like the brake pads is unavoidable).
I hope this can clear up some fear of the unknown. But still, I DO NOT recommend average daily owner go tune the car, unless you are absolutely sure that you want it, or you know what you are doing.
Also, you can always flash the car back to stock whenever you feel like to.
Back to the choice (VR6 or EA888?):
Anyways, since this post is asking about VR6 or EA888, it's obviously down to personal preference. Me choosing the EA888, I prefer the earlier available torque, and don't mind that few horses short. Also, fuel economy wise, EA888 can easily achieve a 30+mpg with highway speeds. And of course, APR-availability is an important factor.
For the VR6 models, I like the fact that it is officially claimed to be able to tow 5000lbs and VW dealer can install the hitch. Or some models can have hitch and wiring pre-installed. That's a very big plus.
To be clear though, EA888 Gen 3 DOES NOT require premium fuel. I once fed it with AKI 87, it was fine and no CEL. I feed it with AKI 89 regularly. Only recently when I had to tow about 3000lbs and I feed it with AKI 91 or 93 (when available).
FYI, the max engine output claimed is usually tested with either AKI 91 or AKI 93 fuel. If you feed the VR6 with 87, it will be a couple of horses short, probably similar to a stock EA888 fed with 91 or 93. (I don't have the exact data, but I've seen tests with other sport cars regarding fuel grades)
For towing,
I had the 5000lbs rated hitch and wiring installed by U-Haul and I recently towed about 3000lbs for more than 1000mi of highway, city, uphill, downhill in dry, wet and snow conditions. Everything was fine along the trip. I travel about 60-70mph on the highway and had to frequently stop in the cities, and surprisingly it did a 15mpg combined.
And I was actually surprised by the EA888 and the 4 motion. I mostly put it in normal mode along the way. For a couple of times, I had to stop at the uphill intersection with inches of snow or slush, with the 3000lbs trailer, the car can easily pull off and I didn't feel any slip at all. I'm on the rather rubbish stock Goodyear Assurance tires. I checked, it was the cheapest variant, with only 5 of 10 of snow performance from Tirerack.com. I was travelling after midnight, so roads weren't cleared yet.
If you tow heavy stuff frequently, please GO with VR6, as it is officially supported by VW. EA888 can tow, but it is not officially supported. VW dealers will not install the hitch for you.
But I'm curious, hardware and software wise, what is the difference? Is there any specific tweaks that damage proof the vehicle while towing? Anyone who knows about this are welcome to comment.