The DICOM standard process heavily favors leveraging existing standards. When work on the JSON encoding began, we had an existing XML encoding (from WG-23 app hosting) so that design was mapped to JSON. BulkDataURI can be used to downloaded binary items separately and as binary rather than base64.
http://dicom.nema.org/medical/dicom/current/output/chtml/part18/sect_F.2.6.html
It is assumed that server implementations would choose to inline base64 small binary data items (e.g. less than 128 bytes) and externalize BulkDataUri large data items.