I think it just might be easier to take an expectation value.
If mask region 2 has 50 voxels and mask region 8 has 150 voxels, I could just use any old math program to make an average between the two colum vectors that 3dROIstats would generate. I'm sure I could trick 3dcalc into doing this for me with some scripting...
[(50 * index j in mask value 2) + (150 * index j in mask value 8)]/200