Sorry, I didn’t quite understand the problem at first. The luma matte for the glass is cutting out the reflections, because they are transparent in the layer without the reflections. The reflections pass requires a different alpha channel from your 3D app because different areas of the reflection layer need to be visible.
In other words, each rendered pass needs it’s own alpha channel to cut the proper areas.
Walter Soyka
Keen Live, Inc.
Digital Media Design & Technology