The OP stated that the tests were run at the same resolution. So that doesn't seem to be the issue...
I would agree that Microsoft had to do something to compensate for the SP3's design. Given how much attention they paid to engineering the fan assembly, it's obvious that thermal performance was a concern. And really, I don't blame them: personally, I'm happy to accept somewhat lower performance in exchange for the SP3's form factor. And, further, I think it's a mistake to buy the SP3 with the intent of using it as a gaming system (or, e.g., a video editing workstation). The form factor--larger screen with a better ratio, thin, light, decent battery life--makes the SP3 a superior productivity machine, which is precisely where Microsoft is targeting it.
The thing is, I don't see Microsoft marketing the SP3 as a gaming or processor-intensive-application machine, and so there's nothing deceptive going on. I think some folks want the SP3 to be something it's not, and indeed I'm not aware of a single Win 8.1 hybrid that's significantly better in these areas. If someone wants a good portable gaming machine, then there are far better options out there.
I don't mean to be dismissive of the OP's concerns. But in this case, I do think it's valuable to mention the old adage "the right tool for the job."