Engines are most definitely broken in on the dyno.
This allows the wear surfaces to bed in in a controlled manner, normally with special engine lubricants which are changed along with all the filters after the initial running in.
At the same time each cylinder is individully adjusted to operate correctly and the engine performance in terms of output, heat rejection, friction, etc and health parameters (fluid temperatures, pressures etc) are documented and must satisfy certain criteria for the engine to actually go on a race car.