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Square holders are the most affordable option with the least amount of uncertainty. Additionally, they will make cell manufacturing easier as compared to the other options. If the chosen cell arrangement is available for purchase as a pre-made module, it will most likely be cheaper to choose that option, and will probably save weight and manufacturing time.
Update
Since we've deviated from this significantly during our design, I feel like this page now requires an update. We went with CNC-Machined (actually 3D printed by Linamar, but the original intention was to CNC machine) plates that got attached to the cells and had holes for heat-set inserts to attach the aluminum standoffs, gusset plates, and module PCB together. We also switched to an HCP cell pattern to allow for more airflow along the rows so we can circulate the air in the battery box faster.