The big thing is that the frame is kept square at 4 axis. A loaded suspension will approximate this which may be why people say to do it that way to an assembled car.
However setting the jack stands in the 4 spots I mentioned along with 4 bubble levels and shimming the frame level along those 4 axis makes real sure that frame is square. A vert you would want to add removable bracing near the door tops to hold that front to rear door gap when sub framing it.
