It is much more advantageous to me if KIX-ORD-BOS (on a single flight number) is considered a single sector for RTW purposes. KIX-BOS is about 500 miles less than KIX-ORD-BOS, and I very much need that savings to keep a trip under 29000 miles.

I'd raised the question because the RTW calculator counts such flights as individual sectors. We all know that the RTW calculator is a useful tool but not an authoritative guide; still, when the question isn't covered explicitly in the rules, it is best to find out for sure.