Turning off alpha is a performance optimisation, which apparently can make a difference to fillrate-limited devices. It means the backing canvas doesn't have an alpha channel so the alpha components don't need to be filled or processed or composited to the screen. On platforms where there is typically nothing that can appear behind the canvas then the runtime sets this mode to allow the browser to optimise it if possible. This isn't limited to node-webkit - it's also used on Windows Store, Crosswalk and PhoneGap apps for the same reason.
I guess your plugin needs to force alpha enabled on all platforms, but I don't want to just turn it off completely since that could de-optimise it even when unnecessary. So for the next build (in r188) I added a flag in the runtime you can use to force alpha mode enabled: set runtime.forceCanvasAlpha to true. You have to set that in the plugin or type constructor, since by the time you get to an instance's constructor/onCreate it's already read the value to initialise the renderer.