I connected USB-RS485 adapter to PC and used the same python script. Speed was 2,5Mbit/s (and can be higher I think).
Same Driver? I believe the Due uses Windows built-in CDC driver, which is reported to be "not that great." If your USB/RS485 driver has an FTDI or other chip that has its own driver, direct comparisons could be invalid.
Could be fun to poke at the Due code and see what changes have any effects...