Bakyt,
The USB ground is not the same as the ground of the input or output. If you have non-floating (ie non-isolated) equipment hooked up at the output, that shares common earth/ground with the USB then there would be a ground loop through the CR and it could be damaged.
Same is true for input, if you power your DUT from an earth/ground referenced power supply, and you have a PC hooked to USB (also powered from mains) and/or a mains powered scope/DMM at the output, that is also a hazard condition.
However, if you have a LAPTOP running on a battery, then there is no problem outputting via USB serial, since the laptop is completely floating with respect to the rest of the circuit.
So only 1 common ground referenced circuit is permitted to be connected to the CR at 1 time.
I explained this in the guide, but I hear questions like this again and again. Folks are hooking up batteries wrong and smoking the charger circuit - and are asking for help in this forum, is the excitement so big that users skip the guide alltogether?