When adjusting the position of cue boxes, if a cue's text track cue snap-to-lines flag is not set, step 2 says 

"Position the boxes in boxes such that the point x% along the width of the bounding box of the boxes in boxes is x% of the way across the width of the video's rendering area, and the point y% along the height of the bounding box of the boxes in boxes is y% of the way across the height of the video's rendering area, while maintaining the relative positions of the boxes in boxes to each other."

I thought the line alignment and position alignment would be used to determine which point in the cue box is specified by the positions, rather than using the line and position values as the anchor points. Is the spec just lagging behind here?

The alignment values are used above in step 7 when computing the x-position and y-position. However, when we get to the step of adjusting the boxes, these values appear to be discarded and we use the algorithm described above.