That was a lovely breakdown - and with lots of helpful information too.
First, I suspect there's quite a lot of glare bouncing off your darks, so I've tried to correct that a bit, which leaves us with sharp-edged leaves, which is good. But they're all the same value. That doesn't suggest depth - other than a single layer. So, before I go for a haircut, I'll play with part of it for while
Having begun by making some of the black areas more solid (which I think is due to glare, not inconsistent shading) I just tried to add what I thought I might see if I was looking at it in real life. And changing some of the flat shapes into more three-dimensional ones. Also I think you might be over-thinking it. Try to just create what you'd expect to see.
MARY-butterfly-leaves004.jpg
A: The starting point (blacks a little more solid)
B: Area 1 is slightly darker than 2 and 3, but overall there's one layer of depth (not including the foreground).
C: Area 1 is now on an inclined plane, or in the shade of the lower left foreground leaf - its right-hand end is a little brighter; its left-hand end disappears into the darkness. Area 3 is definitely now behind Area 2, creating at least two layers of depth.
D: Is the same as C with the addition of background stalks and part of a leaf. And I slightly altered the highlighting of the lower edge of 1. The additions are behind Areas 1,2, and 3 - creating three or even four layers of depth.
All edges are sharp. I could push the stalks even further back, and they'd still be visible.
Those solid background blacks tell us "this is the absolute background". So we understand everything else to be further forwards. And, of course, the darker those black holes are, the deeper we can push anything into the shade, and you can create more layers of depth.
Personally, I enjoy inventing shapes in these dark, shady areas. And, my intention is that those shapes don't attract attention... but, if you look into an area you'll see them, and see that the depth goes on and on - just like in life.
Now, you might be thinking, "but these are just leaves. All this depth creation isn't really necessary"... but, once you get your head around the creation of layers of depth. You can apply it to anything, such as hair. You use the foreground to tell us what the subject is; then use the midground and background to show it has depth. Not depth you can necessarily understand, but little in depth is fully understandable in Nature.