Given the uniform shape of the hole and surrounding damage and the fact you were alone on the road, I would think this was deliberate. As you have said, stones don't hover , a common misconception on motorways is that stones 'fly' through the air, in fact, they are thrown up and drop pretty rapidly, driving into them at 70+ mph causes the damage.
I would certainly report the matter too, if that had gone straight through the consequences don't bear thinking about.

The video below shows a very similar appearance around the 'crater', granted this is a 'proper' bullet and bullet proof glass but is shows the damage profile, the ring is from the dissipated energy.