Does each bit represent the existence of a tree at the given cell ?
Yes, and you need other bitBoards for the calculation of actions, shadows and rewards. (one per size)
In that case do you have one separate integer for each treesize/owner combination ?
I have an isMine bitBoard, but you can also separate, it’s a choice to make.
How do the 1/8/9 shifts you mentioned work here ?
Here is for example the projected shadow of 4 trees of size 1:
