Theoretically, having the supports under the ball joint would simulate having the wheels on the ground, which is a requirement for alignment.  Alignment changes as the wheel travels up and down, so you want the specs set at normal ride height.

That brings up the downside of doing it without the wheels.  You cannot roll the car to settle the suspension.  Maybe if you used a floor jack with wheels pointed perpendicular to the centerlne of the car, the suspension could settle to static ride height.  If you jack up the car with the wheels on it, the wheels move inboard as they drop.  When you set it back down, the wheels cannot slide sideways to allow the suspension to settle out to static height.  That is why they use the sliders.

I am also wondering if the extra leverage imparted on the control arm by the tire being farther outboard than the floor jack would cause the suspension to settle better with the wheel than with a jack.  I will have to ponder on that part for a while.

I always find the two best wheels and tires I have an put them on the end I am aligning. I check for runout and outside diameter. I make sure they have the same pressure. I have a fixture I made from a carpenters square that I use with a machinist level that is accurate to a few arc seconds. My fixture has adjustable blocks that I can line up to contact the machined rim of the wheel. I put 5 bags of softener salt in the drives seat to sorta match my weight and settle the car out by rolling back and forth before any measurements. Yes I see a difference if you do not settle out. So using a jack without a wheel is not an option for me.