ID Matte Problems with RPF

I've got a scene with five flat silhouettes. Each silhouette was created via material by using a b&w bitmap mask in the opacity channel. I'm trying to save out an RPF that will give me the flexibility to alter the color of each individual silhouette in post, but I can't get the transparency to play nice when using ID Matte in After Effects. Any place where there's overlap--a transparent portion of one plane overlapping the opaque figure of another plane--the ID also captures the overlapped area of the adjacent figures.

That's a long way of saying, "Is there any way to get RPFs to respect transparency and overlap in regards to obj ID and/or mat ID?"