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I isolated the code changes into a branch and started a new pull request.
This add 3 flow control modes:
RTSCTS - classic RS232 hardware flow control.
RS485 - RTS line goes high only when there is data to transmit (to enable a RS485 transmitter). The CTS line has to be looped back from RTS (this allows you to insert a delay so the transmitter can activate).
IRDA - Isn't a flow control mode, but I didn't want to waste a state. Enables IRDA encoding. The polarity is setup so it can be looped back to itself. It should work without glue logic with the transceiver listed in the code (but I haven't tested it).
There is a test case in the torture test. I've also done testing from python.