I remember reading that there was some paper by one of AMD's highest level graphics engineers describing a Zen APU with a big graphics chip alongside it due for 2017. Now obviously roadmaps can change, but this at least shows that this possibility was certainly in mind at AMD.
Also check this out.
http://wccftech.com/amd-raven-ridge-apu-vega-zen-hbm-2017/
I don't expect Scorpio to possess any kind of HBM, and instead to have GDDR5/GDDR5X or something like that. Although if it potentially DID have HBM, that would actually free up a good bit of real-estate on the SOC for whatever that would be worth to Microsoft and AMD to look into. But then we also did see a shot of the Scorpio mobo at E3 last year, but I do wonder if that was just one of many potential designs, as opposed to anything that's anywhere close to being final. After all, we were literally an entire year and a half away from the thing's release when Microsoft showed us that.
I think Scorpio will have Vega but it won't have Ryzen. I think the main reason will be price, looking at the early sample benchmarks Zen is basically Broadwell level IPC and 8-core Zen is not coming under $500.
I don't really see this as much a strong argument against the possibility, because, for one, Scorpio's version of Ryzen wouldn't be clocked nearly as high as the PC enthusiast class chip. Second, a company like Microsoft would likely not be paying $500 to get their hands on Zen. They will pay much less than what the average consumer would pay to get something of equivalent capability. Third, not only would clock speed possibly go down by a reasonable degree (it's a console after all), but you would possibly also be looking at decreased cache sizes, and potentially even the disabling of Simultanous Multi-Threading. Although, I really do think that if Scorpio does in fact end up with Zen, I also believe SMT is a strong possibility because I believe AMD will use SMT in all versions of Zen CPUs, minus the most ultra low power devices. I feel everything else, from laptops etc would come with SMT activated.