Ecosystems populate vertically "from above", from positive z,
like falling rain.

If one does not want to (or can not) "eco-paint" the thing, turning it around,
I think that one has to work with duplicate objects,
turn them, populate, turn them back,
and make transparent their underlying texture.

I tried with mixed materials (several ecosystems in one texture) to avoid duplicate, triplicate objects, 
it works, somewhat - rotate the object, swap materials, and populate the next sub-material -
but I got difficulties to control that the way I wanted to...:-(
So I went back to duplicate objects.