Threr is a big difference in the mesh representation. If you optimize mesh the results will be more accurate and closer to each other.
FDTD usually use simple cartesian grid (you get something like sugarcubes). CST has better meshing at this case. If you want to see the difference, change the meshing in CST to hexahedral - staircase (in special mesh properties).
I simulated aircrafts with FIT (CST) and FDTD solvers (i think big and complex enough to see some difference). However if you do the meshing correctly the difference is relatively small and insignificant.