I finally had a moment to have a look. The reason why the depth in both of the renders is incorrect is due to the Opcaity Mask Clip Value in the glass material being set higher than the opacity. This will clip that material out of passes like depth and alpha in an effort to save resources. If you set that value to 0.01 or something small you will see that your passes render correctly.
That being said, why they are different between the pathrtacer and deferred when being clipped by the opacity mask is something we need to look into. In the deferred path the actors with this materials simply are not visble in the render. In pathrtacer they are visible but reporting incorrect values.