I don't have a Surface Pro 3 and a dock, but I have a Surface Pro 2 and a dock. Regardless whether I turn on my Surface Pro 2 with or without the dock, the system process doesn't seem to take up any significant amount of CPU usage...it was fluctuating below 3%.
Then again, the fact that your dock connects to your Surface Pro 3 over just 1 disguised Thunderbolt port (that's what the charging port is), whereas my dock connects over USB 3.0 AND Mini DisplayPort, could make a difference. Also, what I have connected to my dock could differ significantly from what you have. I have the following connected:
- BluRay Reader, DVD/CD Reader/Burner Drive
- Diamond USB 3.0 hub with gigabit Ethernet (my on-the-go docking solution)
- 1.5 TB FreeAgent GoFlex portable HDD (connected to USB 3.0)
Either ways, it sounds like a normal behaviour. 'Cause the more devices connected to the Surface Pro when it wakes up, the more devices it would need to initialize for use.