Hello. Sorry for the long-ish post with some digression into lenses, this is my usual thought process. Also my first post on CR. My professional photographic work so far, has been mostly aerial photography (although one of my landscape night shots done from the ground, has been published in Outdoor Photographer magazine...and via a lowly crop body!)
I can sympathize that the OP might have a problem with gear snobs who feel the need to slam the 6D. But let's not be too quick to judge something we haven't tried ourselves, ok?
Was the OP's picture a true test of AF speed or accuracy? Mostly, no (depending on where the lens was focused just prior to the shot). It was more a test of having adequate shutter speed. But I'll dig deeper now.
As for razor sharpness at infinity focus..."always" being easy to achieve via phase AF, I disagree. It depends on the lens and body combo (never heard that before, have you? joking!). I've found there are certain lenses that are difficult to get sharp AF at infinity, even if they are focusing accurately at a closer range such as 20 to 300 feet. As for manually focusing at infinity...that just doesn't work...because the elements always creep, even over a period of seconds. In the old days, lens focus rings stopped at infinity...for some reason, they don't anymore. But then, that was film, and "sharpness" was always hit or miss.
I personally find myself mostly using the non-IS 70-200 f/4L, for my aerial work, with center AF point selected. It is extremely accurate at "infinity" focus...and sometimes I almost think it distinguishes between a distance of 1/3 of a mile, and 2/3...even in the middle of its zoom range.
Having looked at the OP's picture, and his description, several things should be obvious (some of the above responses have missed these). Yes indeed, he was in another airplane at similar altitude, shooting through the window glass (you can't open windows in a jet) passing the other plane going the opposite direction (hence the "closure"...haven't any of you watched "top gun"? Haha...they also had 900 knots closure, as I recall...and neither side was exceeding the sound barrier at that time, nor would they need to...it's all simple math. The sound barrier is actually slower at altitude...but I digress.)
The second thing that is obvious to me, is that yes, given the size of the airplane in the shot, indeed there is cropping going on. He was using a lens that only went up to 105mm on a full frame camera...not a 300mm lens on a crop camera...
As for softness due to atmospheric conditions...not so much. The sky is clear, the air is very thin, the distance is relatively close. Atmospheric blurring looks to be near zero here. The only blur that would obscure the shot, would be the glass layer of the window. It's also possible he chose not to optimize sharpening in post. It kind of looks that way, and it's ok if he wanted to leave it as shot.
As for the 6D's ability to AF on close subjects moving at speed toward, away from, or some combination...relative to the camera...I have no real idea until I try one myself. Obviously it won't match the 5D3, just as the 5D3 doesn't match the 1Dx. One thing I do know, is that the 6D is worth trying. Whether it is worth buying for me personally, will depend on how well I can get it to AF in low light with my lenses, and maybe if I don't like the silly little touch pad. Also a big factor, is the price used 6D bodies will be selling for over the next several months. It seems to me that so far, the 5D3 isn't depreciating very much on the used market, and it's been out nearly a year. The larger price drop has been on new 5D3 bodies, rather than on used ones. If there are several 6D's on the used market this summer, selling for around $1150 US, then in my opinion, the 5D3 new at around $2.6k to $2.8k, is by far the better buy. You're losing less money (or at least a far lower percentage) when you sell, and getting a much better camera as well. Now, for the original $3400 on a new 5D3? To me, no...it just was not worth that price at all. Certainly if it had been 7 or 8 fps and 26 MP with similar noise specs and even better overall speed...then $3400 would have been a bargain...but not as is.