Because there is no limit on the number of Transportory Stones you can build, there needs to be some way to arrange the stones. Them stacking up is just a logical way to make it work. Having too many built absolutely starts making them into a bit of a mess, and I am perfectly fine with that. It is a soft deterrent on building too many. The last thing we need is more hard caps on things.
However, if I could change the stones, I would remove the spinning animations. Because the stones are not perfect spheres, on several occasions, I’ve accidentally clicked on the wrong stone because a different stone rotated in front of my intended destination.