Are you trying to change them when they fall on the ground or when they are in the air?
# BRANCHES AND LEAVES
[OVERRIDE:172:T:TreeBranches:TILESET:24]
# TWIGS
[OVERRIDE:59:T:TreeTwigs:TILESET:29]
Figure out what that means based on the readme.
Seem to be the leaves you want based on this post
http://www.bay12forums.com/smf/index.php?topic=144270.msg5708909#msg5708909, they are still changeable in the d_init.txt file anyways.
So, it looks like you'd need the ability to specify the material in order to change the graphics for Fruits, Pods, Leaves, etc.
These are in the raw\object raws, you can change them there to be what ever you want them to be. It hardly matters as of yet because they are just flavor till Toady actually makes the pods and fruits useable, unless a mod does that.
I'd assume if you want to change all the plants you'd just have to give them all different id's in the raws because as it stands if you do the plant_growth change any plant with that id that uses that id should change to be what ever you told it to change to if you did it correctly. But plants can have more than one Id based on their growth cycle.
You will also want to use the tile overrides not items as items are things that aren't "planted" on the ground but laying above it. Sort of like how buildings (chairs) are items when they haven't been planted. But plants would be tiles. But when the plants are gathered you will use the item overrides then if you want them to look different than what they are set to in the raws.