After further investigation it appears stumps get a CuttableTreeComponent that destroys the environment item on the base sector when it grows. There may be an issue where the root isn't destroyed when the entity is destroyed through certain code paths (directly closed by decay system?), or the tree is cut in a way that the root ball entity never exists (unknown)

Also, if the stump is somehow loaded and destroyed while the environment sector is unloaded the stump will be destroyed without the environment item being destroyed. Also, the stump stores the entity ID of the environment sector, which in older versions didn't change between sector loads, but in 0.7 DOES. This means that destroying a stump after a sector reload will cause the environment item to fail to delete.