the time computing transmission spectrum with no scf in atk-se is much longer than that in atk-DFT for the same structure.
It hardly (never?) occurs in SCF but it can be possible in transmission.
Because the calculation time of transmission mainly depends on the size of transmission matrix, in other words, the total number of orbitals.
For instance, if you use SZ in DFT and Cerda in SE for Silicon, the number of orbitals per atom is 4(s:1, p:3) in DFT while 9(s:1, p:3, d:5) in SE.
In such a case, the calculation of transmission for SE costs time more than that for DFT.