Wait guys, I think we're just stupid.
You need internet connection enabled and your 3DS be connected to the internet for it to work. I just remembered that.
Then I just went back to scan the QR code except with my 3DS connected to the internet, and it worked first try. This is 10.3.0-28U on today's update of the payload.
Either that, or he stealth fixed it without telling anyone and being connected to the internet didn't really matter. The payload still says 2015-11-18 14:46:39 though, I think if it had been fixed then it would show at least november 19th, no?
Unless he's able to fix the QR codes without changing the actual payloads
Before trying with internet on, I tried once again with internet off and that booted me back to home menu and restarted my 3DS, just like it did before. Then I turned on my Wi-Fi and let my 3DS connect to it, and now it works like a charm. Tried deleting save file and rescanning the QR code several times, every time it's worked first try.
Kind of a facepalm moment now x)
That being said
Maybe the Japanese payload has a problem and the US one works fine. Or the EUR one too, since someone reported that one not working right either. I can't really test to see if I can get the Japanese one to work the same way I'm getting the US one working right now.
Though if you were able to scan the 10.2 code and get it installed you probably already have the internet connection so maybe the payloads and the QR codes really are bugged.