You don’t need that assumption. Your assumption can just be “the person and vessel (or a point in the vessel, like its center of mass) don’t diverge significantly over time”.

Then, if you treat velocity as a vector and compute the person’s average velocity vector over time, you’ll have a pretty close estimation to the vessel’s velocity vector.

After all, if those two average vectors (vessel’s and person’s) were to differ much, they would end up in different locations.

The average basically zeroes the vector for each lap the person does, so the remainder must be the vessel’s.