Hi,
hardware flow control is not implemented in the microcontroller, so this feature must be implemented by software using GPIO pins. I'm not aware of an application note or general recommendations about this.
"Basically the setup works, when I de-assert the RTS output of the MPC, the transmission of data stops, but not immediately. It seems that 1 byte is still sent which causes a buffer overrun error on the MPC side."
- The effect is usually not immediate - transmission can be already in progress, so the receiver needs to be still prepared.
It's similar to Xon/XOff flow control. When XOff character is sent, receiver may still receive some next characters because it takes time to send the character, transmitter has to process the command and then current transmission must be finished.
Regards,
Lukas