Yeah, the paper mentions that the only way the authors were able to get reasonably accurate alignment was by manually adjusting the offset during the printing process.

On my printer, the extruder uses a toothed gear that grips the filament by biting into it. The exact length of filament that gets displaced for a given amount of gear rotation depends on how deeply the teeth penetrate, which in turn depends on how tightly the gear and filament are pressed together, the filament's stiffness, ambient temperature, and probably all kinds of other factors.

It seems to me that you could solve this problem in principle by printing a toothed pattern into the filament itself, so that the gear teeth automatically align it to the correct position, instead of deforming it.