dcm2niix does not use the Frame of Reference UID (0020,0052). Anonymizing DICOM images is a delicate step - you want to be careful to preserve CSA data for Siemens. Also, in my experience many anonymizers can completely destroy Philips enhanced DICOM data (the enhanced version is very different from the classic version). Choose your tool wisely - one option is gdcmanon which has the option to use encryption to provide reversible DICOM anonymization. The other option would be to store all the raw DICOM data in an encrypted form and using methods that satisfy your IRB and only share anonymized NIfTI/BIDS data. The NIfTI format is much simpler and therefore easier to ensure that no private data has been leaked.