I’ve been running the demo on the CW305 target with an external measurement station (PicoScope). It worked perfectly and setting up everything took less than a day.
On this setup, it looks like the communication between the computer the board is the bottleneck for measurement acquisition.
I am only able to perform 280 encryption/sec without recording the traces. On targets where I can save the communication latency, I can encrypt and record go up to 6,000 encryption/sec.
To do so, I follow the guide lines of  (Fig. 2) where only a seed is sent to a controller.
Then the controller derives (based on the seed) and sends the inputs for the targets. It looks like such a thing could be implemented on the SAM3U.
Is such a feature implemented in the firmware ? I was not able to find it. If not available, do you plan to implement it ?
Have a nice day,