I'm just repeating a point here, but I think it might be useful to be explicit.

I just flew ORD-KIX on UA809. There was a change of equipment in SFO. I got 6480 miles. Flying back I flew KIX-SFO and SFO-ORD on separate flight numbers. I got 7259 miles for the exact same number of flight miles. So I could have gotten 779 more miles by taking a different flight to SFO, and there was one 40 minutes earlier.
I didn't think about it when I made the reservation, however.

No system has to make sense. I doubt they do this to scrimp on miles -- probably just a historical thing. But it seems strange