I don't see your attached file, but it's OK for the "ghost mask" to overlap with the "real phantom" -- the voxels considered in calculation are only those that are in one mask and not in the other.  That results in "ghost-only" voxels, and "non-ghost-only" voxels.  I guess typically the two ROIs would look like an hourglass on its side and it's shifted counterpart.  So if your ROIs look like that, then you are probably doing the right thing.  You can look at the code in fmriqa_ghostiness.c if want details on how the metrics are calculated (once the original dilated mask is generated).