Surly and Soma use the midpoint of the top tube, and Trek's measuring point is close enough to it if you ask me.
ECR | Bikes | Surly Bikes
Soma Fab Double Cross


Kona seems to expect that if you're going to stand over the frame, it'll be right in front of the saddle. I think that's fair. Perhaps the other companies on your list would share more about their standover measurements if you asked them.

Looks like I was wrong about how consistent manufacturers were in measuring standover, but I'd stand by a second pass answer of "somewhere between the top tube midpoint and in front of the saddle, where you are likely to stand over the frame" -- if that isn't enough to go by after adding the traditional inch or two, it's a good sign that you should be trying out bikes in person and insisting on what makes you most comfortable before handing over your money.