DUE baud rate of 1Mbps.

It's not entirely true that none of the ports can do 1M exactly. The USART ports have an added set of bits that allow you to do true integer divisors. So, you could program a 1/84 divisor and get 1M. But, only some of the serial ports are USART and I do believe the programming port is on a UART not a USART so it can't do it.

I pretty much tell everyone just to use the native port. It is many times faster both for programming and serial and if you run into trouble there are physical erase and reset buttons.