Okay ... combining what I just read in my own copy of the MY10 Owners Manual, together with the observations and knowlege of Aircon, x250x, LEX51S and others, here's what we know:
MY06-MY08: By default, remote control can open AND close windows. Owners Manual is vague and misleading.
MY09-MY10: By default, remote control does not operate windows, but a dealer can configure the remote control to "open only", "close only" or "open and close". Owners Manual states this fact at one point, while being misleading at another.
MY11: By default, remote control does not operate windows (Duy's experience), but Lexus of Parramatta says it can be configured (after initially saying it couldn't).
@Duy, after seeing the dealer, does the remote now work the way you want it to?