I know what you are talking about, I made a test on a daily timeframe and the points and figures X and O are not aligned. Since this kind of chart is not related to time passing by, I suggest you use the 1 tick chart which is the most accurate for non-time related price representation (such as renko for instance).
In the below picture, you will find that the symbols are correctly aligned when using the percentage setting, on a 1-tick chart.
I’m afraid there is no way to set the points and figures chart to a dynamic scale with ATR, sorry for that.