BOS-SFO (direct)
2,704 miles posted for years by MP
2,700 miles per your tool
BOS-:LAX (direct)
2,611 miles posted for years by MP
2,608 miles per your tool
BKK-NRT
2,887 miles posted for years by MP
2,889 miles per your tool
I am sure every other city pair is off.
Not sure where you are getting your data?
Through flights are way off, ~ 100 miles or so.
I think the PDF timetable is a lot more accurate?