Justin,
I don't have any experience with your error, but from Googling it, it seems to be a Mac specific issue. Several suggestions are offered  here: https://stackoverflow.com/questions/6666... That addresses this warning "WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested", and I hope that would fix the subsequent errors of "chmod: Invalid file mode: =777" and "Error: mclmcr initialization failed" issue with the Matlab runtime. 

Hopefully this will correct your first example, but I think your second example wouldn't work either way, based on "Warning: Interslice distance varies in this volume (incompatible with NIfTI format).". If your DICOM can't be converted into a .nii file with dcm2niix, then it won't be compatible. If you have some other converter that successfully makes a .nii out of it, you could run that externally and create a new de-faced nifti with mri_reface, then convert that back with ADIR_nii2dicom (but using it with the old DICOM may not work, since it still has the original issues that caused it to fail with dcm2niix).

Hope that helps!
Chris