My advice would be to contact the manufacturer and request data on the performance of the machine in this regard. I can imagine that flatbed printers might perform better w.r.t. job-to-job alignment due to (1) their intended application, which includes media/objects that cannot be trimmed after printing and (2) the fact that they're usually aimed at a higher segment and are significantly more expensive, which can be seen as a proxy for better engineering.
Having said that, the flatbed printers I'm familiar with do not appear to be the sort that I would associate with your workshop. They're optimized for productivity, not necessarily image quality. But my familiarity with them is superficial, I admit.