The FD's additional mass is probably down to cheaper materials e.g. steel instead of titanium (Ti is 65% the density of steel and a similar strength) that and the FD is designed to get troops and equipment onto a planetary surface and unload them without station facilities, so the cargo handing equipment could account for a substantial amount of the "unexplained" mass.
I suppose it could even be considered a throwaway ship, get the load delivered and if the battle is won another FD will pick up the survivors.
Well the Anaconda is in fact a Cargoship