Alright back with some more results on the Shield.
The app I was using turned out to be giving me incorrect readings, so I figured out how to get readings right off the kernel itself.
I shall let you come to your own conclusions.
First run from fresh start these are GPU readings:
http://puu.sh/tfsJG/2df39dff3c.png
3 ~ 4 minutes into the GPU benchmark:
http://puu.sh/tfsYF/af2223ec4d.png
What does this mean? It does actually run at 1GHz initially, but then it lowers gradually to the lowest point we see here at 768Mhz - probably why Nintendo choose this speed as it allows for at least a consistent clock speed without it thermal throttling. And this also matches what the Dolphin developers see with the GPU on the Shield.
I'm going to try to push the CPU and GPU as hard as I can and see if the CPU does indeed throttle, but it looks like it doesn't so far as to keep the console game ports on the Shield to run at consistent speeds.