What you are measuring is not bean density (which is the mass of a bean divided by it’s volume), but rather bulk density - which includes the void space (pore space) between beans.
Bulk density is as much dependent on the shape of the cylinder and how you’ve put the beans into it, as it is on the shape, size and density of the beans. Consider that the bulk density of small low density beans could be the same as that of larger, more dense beans. Likewise, beans of variable size / shape will typically have greater bulk density than uniformly sizes beans, assuming the same bean density.
That said, bulk density might still be a useful measurement when coupled with bean density, as both density and size will influence roast dynamics.
One way to determine the bean density (if you don’t mind wasting some beans) is to fill the void space with a liquid (oil or water - something not absorbed into the beans). This will allow you to determine the volume occupied by the beans (by using the liquid to determine the volume of the void space), and thus their mean density.