Since this soil is loose, and I think there will be no significant soil attached to the tuber during harvesting, does this underestimate the soil loss washed off under this study?
I think so. Land use and crop selection and the management systems they entails are part of your management. Harvesting of tuber crops change the bulk soil structure and hence the amount of soil loss and this should be considered as a part of your management system,
Of course, it should be part especially when root crop is your test crop. This will enable you to account for total soil loss from the farm ie. soil loss due to water erosion + soil loss due to crop harvest.