They used to tell us at lectures, a couple of decades ago, that the clearing 
agent following the stain serves to raise the refractive index of the tissue so 
that when coverslipped the whole thing, i.e. slide, tissue, mountant and 
coverslip, would have the same refractive index. This would give a clearer 
microcsopic image.
I never bothered to check if this is textbook information or not. It just seemed 
to make sense and we just accepted it.

Carmen 
St. Luke's Hospital
Malta