For one thing neither PS4 or XBox One are what you call "off the shelf", because you can't just go into a store and by an APU like that.
In the case of PS4 you also can't go and buy sticks or a stick of high speed memory for both your CPU and GPU to access at once, nor can your buy an APU with an additional BUS that can bypass your GPU's cache.
These chips are by no means "off the shelf" parts, they're PC like in nature of their core processing elements, with funky tweaks to make it easier for the developers to play around with, but that doesn't mean they instantly no everything that can be done with them, those funky tweaks also opens up the scope of maximizing each system's potential.
The fact of the matter is that features are still present in both systems that need to be utilized to maximize the resources usable in each box.
Early generation games aren't properly parallelizing their code across all CPU Cores to make the most of GPU resources.
The GPUs can handle AI, Physics and Audio, along with Graphics code and fiber based rendering to make the most out of every Nano Second of GPU time is still in it's infancy.
Engines aren't anywhere near what you would call efficient yet.
X86 is much younger than RISC is, people have misconstrued things the other way around, thinking that X86 is the more understood code base or that there's no room for creation of new processing methods, that's absolutely wrong, we've also never had a generation where the majority of the system architecture in a video games generation is using X86.
We're early in the generation, things will most definitely improve, people have barely seen a fraction of what's possible yet.
