If I am reading this correctly, you have each bottle with it's own reflection on a separate layer? If so I would mask each individually (rather than blending) then fade out with a mask on a group. That way you keep bottles in front of each other and without that darkening effect you are showing on the overlap.
Bottles are tricky to photograph, so I always do groups shots one bottle at a time and composite back together. If you are shooting on glass (Which I never do because of the second offset reflection from the underside of the glass) or acrylic, then include the reflection when making the clipping mask, but if you are doing this for a client, then make sure that's what they need. I am always asked to supply PNG files with transparent backgrounds so they can be built up as required in their websites or leaflets.
If you are talking about overlapping reflections, then rather than use blend modes, you could add a layer mask to one bottle, and copy the layer mask to the next bottle and invert it. That gives you perfect alignment of thew two masks. I don't think we have quite enough information to give you better answers than that. Incidentally, if you are getting into that sort of commercial photography seriously, then am loving the Canon 5DS I moved to after giving up on a high res replacement for the 1DsMK3. The 50Mp resolution makes it so much easier to created really detailed clipping masks. You might also like to get hold of Fil Hunter's Light Science & Magic book. It is the definitive work on tricky product photography.
I hope you got to test the product after photographing it Trevor