If using the Layout LOP with instanceable references Is there some way of ‘adding’ animation to individual instances?’
I am trying to create a landscape with rocks, boulders, trees etc falling vertically into place at random intervals.

You can do this either 1) with a SOP Modify, or 2) write your instances to disk, animate them and re-import them.

While the 2nd method is more work, it affords significantly better performance in Solaris. And it's not that much more work.

Here is a demo of both methods. I'm using a CHOPs setup to animate my instances, but you can animate them however you want.
Please allow the 4K versions some time to process.

Using SOP Modify:



Using USD Export/Import and Sublayer: