At a high-level, is the vegetation in this scene (e.g., the grass, leaves, etc.) generated by writing a program that applies randomized transformations (minor scaling, translation on the ground plane or in space) to the core objects?

In some games, we can see find out many reusable instances that occur in different scenes. However they are using exact same copies which leave a bad impression to the player. So I am wondering if the cost of copying a raw object and do some random mutations to make it unique is high? Why there are companies, including big companies, still using the exact same copies?

Interesting question! I would imagine the vegetation that are copy and pasted is part of a library that environment artists pull from. I would imagine once they are placed, it would be hard to algorithmically mutate the objects so that they all look slightly different.