I don't think you can use alphamapped gfx in lsxcommand, I'm afraid. You can only make the entire thing transparent. The only mention of alpha maps in the docs is this:

CommandTrueTransparency BOOL
If set to TRUE, lsxcommand removes Magic Pink (True Transparency).
If not set or FALSE the DesktopBackground is painted instead.
This enables Fake AlphaMapped lsxcommands (if not Hooked and not AlwaysOnTop)

I don't know exactly what you're trying to do here -- visually I mean -- but couldn't you hook lsxcommand into a label, and let the label provide the alphamapped background?

(sorry if I'm not making perfect sense; I just got up)