I wouldn't do this, it's making the render much heavier for no real good reason, just render clouds and glass separately and comp together?

If you really really want to do this then you should just be able to increase you're max refraction rays in order to pass through to the clouds. This also means you're clouds will become a component of the glasses refraction shading function which has the downsides of:

The result of you're cloud rendering is at the whim of you're mia material and how its's shading is integrated.

If you want to make arbitary output variables to control the shading of the clouds in compositing it can be hard ( sometimes impossible ) to generate the extra passes through another materials calls.

e.g. if you want to output the indirect lighting contribution of the clouds to control afterwards how can you split this from the refraction component of the glass output? Some renderers can do this but not all, often will require a custom shader.

Youre render times will have to be longer, and good cloud rendering is already slow.