6.06c is only valid if the ball was caught or was right in front of the F2. This allows him to stay the box on a quick throw. Once he has to chase it the batter has to clear. It would be a straight interference call. At that point it's umpire judgement if the batter indeed in the way or not.
If the catcher tried to draw an interference call the I have a run.
At this point there isn't much you can do about it. He used the wrong rule but got the right answer is he thinks it was BI.