[2021] Once again, when I lay roads, the rocks remain.

It's one of two things depending on the size of the rocks. For large rocks (they're technically buildings) it's collision being disabled, which is usually something you switch on/off through a mod like Fine Road Anarchy 2.

For smaller rocks which are props, it's the settings you have with Prop and Tree Anarchy. Networks and buildings do not remove these props, only hides them, so they're back when you remove the roads or buildings. Enabling anarchy for props and trees stops this behavior.