The CPU in the Pro 3 models are different than the models used in the Pro 2. Even though they are "Haswell" chips, they are built completely different and are not the same type that can be installed in a desktop or laptop (which the Pro and Pro 2 did use). They are flatter in design and wider to actually increase cooling capability (at least, designed to do so) and that may not be the case.
The temperature sensor settings are most likely different as well (as you may have noticed) and in fact, the Surface Pro 3 tablets are first time the i3, i5, and i7 processors are being used in. So, that means there is no track record of actual performance.
The only real difference between the SP2 (4200U) and SP3 (4300U) is clock speed. The processor size is the same between the two.
The throttling max temp can be adjusted usually in BIOS. The problem with the SP3 is not that it throttles but that it throttles even when it does not need to. The anandtech review (http://www.anandtech.com/show/8077/microsoft-surface-pro-3-review/3) shows the CPU throttling around 90C and staying throttled down to around 60C. This is where the problem lies. MS should be able to bring the lower number up to around 80C - 85C with firmware updates but they may not if we don't let them know we want it.
There may be larger cooling issues preventing this but a sustained temp of around 60C is crippling.