I liked it SPOILERS
It was a pretty good movie, atmospheric and haunting, it all made sense to me.
When his real mom died, Jin-seong was told by someone at the orphanage that she became a tree so understandably he liked the tree in his adoptive parents yard. When he felt rejected by them he relied on the tree even more, then it became his grave after he was murdered by his adopted mother and father, and the tree sought revenge on his behalf, maybe it was his mother's ghost inhabiting the tree.
In the end, when LE dug up around the tree, the acacia tree roots had encased Jin-seong like an embrace of mother and babe.