The speed of USB3.x has zero bearing on the speed of programming a radio over a serial port.  Even the first generation of USB (USB1.1) running at 11Mbps is WAY faster technology than the serial port connecting to the radio say at 38400 bps.  That's 0.03Mbps.  More likely, the reason for seeing different speeds of programming is due to delays from the program sending get getting acknowledgements from the radio, serial port delays due to emulation, etc.

--David
KI6ZHD