The speed is dependent on the slowest connection. So ignoring the actual hard drive speeds the fastest you will get is with both drives in the double docking station.
If you have true 3.0 USB ports (blue plugs) they may be faster in theory than the docking station. But the transfer will never be faster than the dual docking station. The speed might be equal, it might be slower, but it cannot be faster. Again think slowest connection.
This might be confusing or it might help.
The numbers below are completely made up for ease of understanding.
Pretend the docking station can input and output at 1 GB per sec
Pretend the USB 3.0 can input and output at 2 GB per second.
Your transfer is dependent on the slowest connection (1GB per second)
Because the slowest point is 1GB at the docking station your speed would be the same whether you used the USB or just the docking station.
Now flip the numbers
Pretend the docking station can input and output at 2 GB per sec
Pretend the USB 3.0 can input and output at 1 GB per second.
Your transfer is dependent on the slowest connection (1GB per second) In this case you would be faster unplugging from the USB and using the docking station alone
But all this goes out the window if the docking station cannot just copy disk to disk an instead must go through the USB to the computer and back. In this case you're still limited by the slowest connection.
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