Thanks, I get what you're saying, the spacers are dished where the studs go to accommodate the lugs. Makes sense.Factory stud will fit just fine as long as whomever made the spacers knew what they were doing. And presumably they would since each spacer is usually custom for a toyota as well as the specific model.
I think it will make more sense when you put them on in person. Look up some YouTube videos for installing 4runner spacers. That should help.