Hi eyebird,
I think you wanted to address Loopix, should mention that next time, but I hope I can help you until Loopix will answer you. The part for the trunk, the braches and twigs on the texture is the upper left quarter. If that is still black and you apply the overlay, the trunk won't be visible.. You should just use the overlay-trick for the leave area..
Greetings
André W.