I am mentoring a student who got his manuscript back and one of the concerns was the running head. My reading for the centering is that the running head is centered within the 40 cells as long as there are 3 blank cells before the page numbering. I think the proofreader's thought is that the centering is based on the cells remaining after the page number has been inserted minus the three blank cells.
Sorry for the delay in responding. I'm never quite sure how to answer these types of questions as I am not a part of the NLS program. However, I can tell you that the heading should be centered on a 40 cell line (leaving at least 3 spaces on either side of the heading). This item IS one of the items up for discussion in our errata process (which has started) for BF. Not to change it, but to clarify it.