Paul,
The current release does not have a command-line argument to replace the template. It's a reasonable feature to add for expert users who can create a template that has sufficiently aligned anatomy but want to match their specific scanners/sequences, but it's not something I'd ever thought of, and I thank you for the suggestion. The only way I can think of is that Matlab's compiled binary `mri_reface` is a .zip and can be opened with .zip file readers, so maybe you could swap in a different MCALT_FaceTemplate_T1.nii with the same name and spatially aligned anatomy, but I'm not sure whether or not Matlab's runtime libraries would refuse to run it. There's probably a checksum or something like that. 

We are currently validating a new major version/feature where the replacement voxels much better match the intensity profiles of the original, and the early results are very promising. I think this will meet your needs soon-ish. For 0.3.x, it's true that sometimes the replacement face voxel intensity could be better matched in some sequences/tracers, but we've also found this to have pretty minimal effects on brain measurements and the deviations are still smaller than with other programs that don't really attempt to match the intensities in the first place.

Chris