Justin,
I don't think I want to make this change for everyone, and it seems like something that wouldn't have enough usage to warrant making it an option at the top levels of the run-scripts, so anyone calling it would have to modify some code at one level or another in order to use it.

However, unlike the core of mri_reface, ADIR_nii2dicom.py is open source.

If you look at line 665:
metaOut.file_meta.MediaStorageSOPInstanceUID = pydicom.uid.generate_uid(prefix=uid_root)

you should accomplish what you want by copying this and changing it to

metaOut.file_meta.SeriesInstanceUID = pydicom.uid.generate_uid(prefix=uid_root)

Does that work for you?

Best,
Chris