Yes, through the state option (xdotool calls it windowstate). I was confused when implementing it, because there appear to be three different fields: maximized_horz, maximized_vert, and fullscreen. If you want total fullscreen (covers taskbar and other stuff), use the last one. If you want the window maximized, use both of the maximized ones.

Come to think of it, I should put in better documentation for the state option, as well as a general maximize alias.