Glad you liked the paper and thanks for the great question!
The casts of the rooted teeth are in fact larger than the shed tooth casts, but only by the addition of the root. Actually, the tooth crowns from the shed teeth and the rooted teeth are the same - the only difference between the rooted tooth casts and the shed tooth casts is the root-portion itself. This is technically a different size, but it is more of a change in shape. For example, the Allosaurus tooth crown is more or less conical in shape while the root-bearing Allosaurus tooth is more elongate/cylindrical due to the addition of the root portion.
As you indicated, this will add mass to the root-bearing casts. So the question comes down to investigating the roles of mass and shape in transport potential. Flume studies like the one in this paper have been conducted on a variety of vertebrate remains (i.e. Coard, 1999; Coard and Dennell, 1995; Boaz and Behrensmeyer, 1976; Voorhies, 1969; Peterson and Bigalke, 2013, etc) and shape has been found to play a more significant role than mass in many cases. This is especially true of flat objects (a scapula), which are less-likely to become transported in fluvial systems than objects that have lots of processes that stick out in different directions (a vertebra). Flowing water is more likely to flow over a flat object but an object with processes will catch and get pulled up into more turbulent flow. These objects may have similar densities (mass by volume3^) and size, but the shape plays a key role in transport. This is not to say that mass and size play no role at all, but rather that shape plays a more significant role in transport. Further studies may reveal more on the boundaries that each of these factors play.