In my experience noise on hot-plugging the serial adapter is a complete nonissue. I'm sure it matters for you, sometimes. But for this kind of embedded work, I'd say it's important far, far less than 1% of the time.
I assume the possibility of spurious Rx state is why FTDI chose to wire Rx to the tip pin of the female TRS connector: It's the last pin to make contact with anything when plugging in, and therefore least likely to be bridged to ground. I suppose the mechanical design of any particular jack would determine whether it's possible at all.