kz is not a good quantum number since we don't have periodic boundary conditions in the Z direction. And besides, your expressions only hold in the free electron gas approximation. The correct picture is quite different.
The conserved quantum numbers for elastic, coherent tunneling are kx, ky and the energy e (I use lower case here to separate it from E later on). The transmission coefficients are computed for each energy, kx, ky separately. Given a particular value of these, the inverse problem can be solved, to determine the possible values kz such that
E(kx, ky, kz)=e
where E is the "band structure function" for the electrodes (actually, the complex band structure, which can be computed by ATK and plotted). Some of the values kz will be real (propagating), some will be complex (decaying modes). For each mode (both real and imaginary) the probability that it will be transmitted to the other electrode is computed, taking also into account whether there are any matching solutions in that electrode - remember the electrodes could made from different materials.
In reality this calculation is not carried out this way, the whole thing is done with Green's functions and self energies, but the result is the same.
The sum of the probabilities is the total transmission coefficient T(e,kx,ky), which can be >1 since it's a sum of possibly many probabilities, each one of which is <=1.
Finally, the sum (integral) over the Brillouin zone gives the total transmission
T(e) = int T(e,kx,ky) dkx dky
which thus also can be >1.
Both the transmission coefficients T(e,kx,ky) and the probabilities for each mode (the so-called transmission eigenvalues) can be extracted from a calculation in ATK.