Quote: "Why would I ever want to add a transparency command to a FPE file of a tree?"
It depends on how you make your trees, the common way to make trees is to use a plane for a clump or bush of leave, that plane will be a flat square with a texture of the leaves on it, the texture will be transparent wherever it doesn't have leaves, those need to have transparency set.
The transparency "command" (it's not a command it's a setting) tells the engine which layer to render the transparency.
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