It IS possible but I'd not recommended it...
Best if a Component's base geometry is left on Layer0 and the Instances are placed on Specific Layers in each Model that way you can have some 'trees' on and some off by having them on TREE-PH01 and TREE-PH02 layers for example...
An outline to do what you want is a tool you run and it asks you for a folder to process, starting in the Components folder. You navigate to say your 'Trees' folder and pick one of the SKPs in there.
Now it knows which folder to process.
Now asks for the Layer name - it could read the base-folder name and capitalize it and truncate to 4 characters to suit AIA standards etc - in the dialog you [accept or] enter a name - say 'TREE' for the layer.
It then imports each SKP file in turn as a Component.
It takes that Component-Definition's entitles [and any sub-component-instance definition's entities ?] and puts them onto a Layer called 'TREE'.
It then exports that Component back into the same location, overwriting the original.
All SKPs are processed.
You do a folder of similar Components at a time. You might need some pre-processing thinking and say split your Planting into folders like Trees, Shrubs, etc IF you want separate layers for these...
My import_from_folder.rb is an example of how to import files... perhaps more applicable my batchEraseFlatInstances.rb which does something similar to what you want, BUT that goes through a list of SKPs in a selected folder - imports them, edits them to erase 'flat' instances within them and then does a save_as on the definition back to where it was...*
The changing of layers etc is also to be found in many scripts available here and could be substituted for the erase 'flat'... part of this script*...
