MNL-SIN-PVG counts as 2 flights to the flight segment limit and approx 1474+2357=3831 miles towards total mileage limit.

You can start and end at different airports within the same country. In this case the mileage between start and end location is not included. No real effect within UK (unless you are close to the limit), but potentially a big saver in wide countries like USA, Australia. Note you may also be able to use city codes for some flights instead of airport codes - eg TYO-OSA is considerably shorter than NRT-KIX.

The airlines have their own distances they use. Mostly they will be close to the distance on great circle mapper (or a timetable) but not always.