This is a problem, shure.

I might just make a very simple sollution, and use a brush to paint them by hand,
if nothing else works.
The trunk is rendered correctly, And the leaves caste a much lighter shadow than the trunk.

Another thing would be to insert a dummy model onto the trunk during the shadowrendering, that
has leave-polys.

The shadow is not as hard edged as the stencil shadows, so the player will not
notice a big difference.