Ok I just looked at the pictures and it's right there in the first picture the portion you circled. TR=on /off

Also the warning is saying what I suggested that if the low/high is wrong there is position shift and you'll have errors. Every direction change you'll lose one pulse.

Don't think pokeys supports this but not used one for while so not sure but if possible wire step/Dir differential rather than Common Anode or Cathode.