Michael, as others have suggested, if you are going with a bivy, I think you would be much better off with a quilt of some sort. For the same weight as the atom a quilt would be comfortable over a wider range of temps. I haven't used the Marmot Atom, but all the reports I have read indicate that it is comfortable to 40F for people who sleep warm. Someone I chatted with earlier this year (who thought they weren't a particularly cold sleeper, said he wasn't comfortable in the atom below around 50F without wearing extra clothing).
As to combining the spinshelter and the BMW vapor bivy... I think it might be overkill. The spinnshelter in a lock down pitch should not only protect you from side-blown rain, but also from wind. The only thing you would need to worry about is standing water. I have successfully weathered a number of nasty wind/rain storms in the spinnshelter, using a quilt, without a bivy. Of course, the spinnshelter in lockdown cuts you off visually and venting wise as much as a closed tent, losing some of the natural advatages of a tarp.
On the other hand, the bivy gives you a lot of options. I have mostly stopped using my bmw vapor bivy after I switched from a poncho/tarp to the spinnshelter. I have been considering selling it on ebay, but I have also been considering holding onto it because the combination of a silk liner, my quilt, and the bivy give me a very wide range of conditions where I am comfortable, and for many conditions I don't need to setup my tarp.