Alex, I think you are reading the exercise incorrectly. From your description I assume your root is C. Are you aware that this specific exercise is descending only? Therefore it goes from the highest 3rd (E) on the 1st string down to the 6th string and does NOT ascend from the 6th to 1st string.
In the Calisthenics, when there is a “down” arrow on the left, the exercise only works descending; if there is an “up” arrow, it only works ascending which is the case for the 3rd and 4th exercises. All other exercises are to be played descending and ascending as in the videos. Is this what is throwing you off?