The GUI-based batch patron upload form allows for selecting a match point, neither of which is the Koha ID, as an external system generating patrons is not going to be Koha-aware. Yet the REST API now requires knowledge of the patron's Koha ID to update a patron, necessitating a manual patron lookup request prior to submitting either an add or update request. For individual transactions, this is cumbersome. For bulk transactions, it's unwieldy. It would be more helpful to have the option to choose a match point in the request, and for the software to intelligently add or update a patron as necessary. This would significantly cut down on the external development necessary to create patrons via API, as well as API requests per patron add/update.
We have implemented a batch update with the current API using look-ups and also deciding on which fields in a patron we want to update. I think you have more control of the process the current way, but what you describe has it's own merits. Maybe instead of using the patron API using the patron import CLI script could be an option for you? It's very close to the how the tool works.