In it's current form one can distinguish 3 steps:

1) converting underlay in AFNI format to NIFTI 
2) resample overlay to space of underlay and to NIFTI
3) generate plot

Indeed (3) could be general, but consider that it requires that the underlay and overlay are in the same space. In a typical use case where underlay=anatomical and overlay=EPI they are not (different voxel size & coverage). As far as I know such resampling is not implemented yet.