If i had to guess the mobile cpu probably has more strict settings and is getting throttled because of heat or voltage or something like that.
Regardless that isn't going to be an issue when using desktop cores.
It was somewhat of a rhetorical question (as I believe you're right about the thermal throttling). The point is the 64-bit Multi-Core Geekbench score for the rMBP is 12,720 whereas the 2010 Mac Pro score is 8,437. According to Geekbench the rMBP should be 50% faster. In reality, when transcoding with Handbrake, it's approximately 30% slower (if memory serves correctly...it's been a while since I bench marked it). If one were to buy a system to perform Handbrake transcoding work based on Geekbench scores they could be disappointed. This is the problem with Geekbench...it's a simple test which is good for making comparisons on how different systems run Geekbench. It could be used as a starting point but that's about it.
System configurations:
Mid 2012 rMBP quad core @ 2.7GHz, 16GB RAM
Mid 2010 Mac Pro quad core @ 2.8GHZ, 32GB RAM