Following the compositing logic, refractions cannot be transparent. The way in which YafaRay should render them - opaque alpha.

Reasons:

1. If you are going to replace something behind the glass - this means you're going to replace refractions. In that case you just would switch refractions off.

2. The shinydiffusemat Material already has everything to render glass without refractions, with transparent alpha, while maintaining reflections at the same time.

3. The common compositing logic assumes that refractions aren't transparent.