I didn't write that WSJT-X doesn't work with SSDR - I run two 6700s, one of which feeds eight instances of WSJT-X and JTA. What I did write is that Hamlib doesn't fully support SSDR - it only supports "VFO A" and "VFO B" - it has no concept of switching between SSDR panadapters and/or slices, so it can't designate a specific slice for transmitting without resorting to COM port emulation for each slice. This was a bigger issue before SSDR and SmartCAR implemented 'Auto TX Switiching' but still causes some operational issues (as you noted) and I'm corresponding with the developers about how to implement a complete solution.
And, as I said, this should be moved to WSJT-X list.
Mike - N8MSA