There is a photo of people playing Killer Instinct on a load of Xbox Ones, so there were definitely some playable machines there.
This really is a non story though IMO. The gameplay will be representative of how it will look in the end (as if it's not, the gaming press will have a field day), but they probably ran it on a PC for stability issues. How bad would it have looked for MS if a game had crashed during the presentation?
There was no devkit/pc on show at E3, every "demo" of the Xbox had a X1 on display and seemingly all(if not most) were simply as most other tech shows at this stage, a box on show with a led powered with cables going under a table to a PC.
IT's bog standard for E3 and shows like it.
As for what PC they used, considering at the moment MS is producing PCs that are Nvidia and Intel compatible(Surface with tegras or Ivys ), MS's contract for a CONSOLE which is a different device, went to AMD. I wouldn't be surprised if most PCs at MS were intel/nvidia and whatever company they have a deal with, HP, Dell, whoever, provide them with PCs with Intel cpus and Nvidia gpus, thats just how life is. When they place an order for a PC it will be with whoever they have a contract to supply PCs from with whatever those guys are using, thats how business works.
Conversely, you could simply say that despite MS using PCs with Nvidia and Intel at MS headquarters.... they went AMD for their gaming console? Doesn't that actually say that when it comes to gaming we already work with Nvidia and Intel, but we went with AMD because they are better?
Can't you also spin it(if you should want to) that a pretty small AMD gpu in the region of a 7790/7870, is able to provide the same graphics a PC with sli 680gtx can achieve?
People see what they want, the most likely situation is that these PCs are heavily overspecced because they are emulating the X1 software/hardware and they are using the PC's they have to run them.
A good question is, if the X1 isn't available till November, is there a single reason the console should be.... in final working state, have loads available, have the OS finished, etc, etc, etc? if the OS and hardware aren't finished by November 21st(is that the date?) then MS are in trouble, if its not ready now..... so what? You can be almost certain that the E3 before the 360 launched had devkits doing the demos, didn't have the OS/hardware absolutely 100% sorted and ready to go, and yet it shipped with a OS and hardware and we had a working console.
What becomes a different matter is, if on November the 21st they can't provide what they showed at E3, same graphics, same performance, same snappy feel of the OS. I genuinely liked what they were doing with more than one app on screen at time, flicking in and out of game and playing with two tv channels, one on smartglass one on tv.... much of that isn't relevant(because of it being the NFL stuff, and me living in the UK and almost certainly not paying for sky IF sky has the same functionality) but I liked the way it worked. If its suddenly laggy, or poorer quality, or buggy on release, that is an entirely different matter.
Devkits or PCs being used to show games at E3 is NOT an issue, it will only potentially become an issue if they can't deliver exactly the same as was shown on the final shipping product, till then, get over it people.