Thanks ACFlyerDE. I thought that I wasn't going crazy. I think I need to find myself a travel agent, as paying some hundreds to them is well worth it to get this locked in and ticketed without further ado.
Playing on the website booking app again last night I see that it basically counts every destination you enter within a country as a stopover, even if you have flights in and out the same day. It is programmed to get people from destination A to destination B most efficiently and the programmers didn't allow for people like me that want to fly A to B via intermediary cities X, Y, and Z to log FF miles, or in this case PQF.
I routinely start DONEX and DCIRXX OneWorld itineraries from Japan, have two on the go presently, so definitely will do the same with Star once I am back in the Pacific later this year.