As of Arnold 5.3, this flag is set automatically by changing the opacity or transmission on a material.

Determines whether the object is considered opaque (transparent). By default, Arnold built-in shaders set the opaque flag automatically, based on whether or not the shader settings would require disabling the opaque flag on the object to render correctly. For example, it's no longer necessary to manually disable the opaque flag to get transparent shadows for a glass shader.

Exceptions are curves and points when min_pixel_width is in use, and OSL shaders.  

More information about Transmission and Opacity can be found here.

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