Hi Josh,
Sure you can, you just have to add multiple UV channels to the feather in OxMeshFromStrands modifer. Then you can have a two shaders: One to drive the opacity of the feathers using Per-Strand UVs and another shader to drive the overal color using the UVs of the distribution mesh instead of Per-Strand. I hope this helps.
Jeordanis Figuereo (Product Designer. EPHERE Inc.)