The relations are being set for one parent object at a time. All relations are one-to-one relationships. Some parent objects have two relational data columns. The relations are being set in bulk in the sense that we were trying to get all of the relations set with one cloud code call, which would retrieve 25 objects at a time, and loop through those 25 objects one at a time to set the relations, then continue grabbing 25 objects until all objects have values for the relation columns.
I hope that answers your first line of questions but let me know if you need clarification.
Also, we are definitely open to setting the relations with a CSV upload, as we did so to upload all of our static data. Could you point to some docs or examples of people setting relations with a CSV upload? Or show up what kind of values create the relation?
EDIT: I found a well-written article you wrote regarding the CSV Relational Upload: