There is no way to do a 4-wheel alignment on a 4runner. But there is a difference between doing a front center line alignment and a thrust line alignment (some shops call this a 4 wheel alignment even though there are no adjustments in the rear but the rear sensors still need to be put on and calibrated). With a thrust line alignment the vehicle is aligned to the thrust line. Your rear axle is straight (hopefully it is). If you were to draw a line coming off the center of the rear axle at 90 degrees toward the front of the vehicle that would be the thrust line. Thanks to mass production these thrust lines are usually never perfect, or zero degrees toward one side of the vehicle or the other. Half of a degree is usually the spread for which the line can be out for a solid rear axle vehicle. Any more than that and the vehicle"s rear tires won't track the same as the front tires (dog-tracking). The difference is that with a front center-line alignment, or center line alignment, you only align to the center line of the vehicle. Center line is usually determined by just the front tires. Problem with this is, you are more likely to get a crooked steering wheel due to the center line not being the same as the thrust line.
Bottom line is, know what you are getting. Ask questions about their "4-wheel" alignment. If they persist that there are adjustments on the rear suspension they are full of it, leave asap. But it may just be their way of saying thrust line alignment.