to see the same result, as in the report, you should take zero voltage and other energy limits:
&PRINT
&DOS
FILENAME device
FROM_ENERGY 0.272240982
N_GRIDPOINTS 401
TILL_ENERGY 0.492829218
FROM_ENERGY 0.272240982
N_GRIDPOINTS 401
TILL_ENERGY 0.492829218
&END TRANSMISSION
&END PRINT
The Fermi level is 0.38253510. The result is in attachment. It is not exactly the same, but it can be for many reasons.
I am currently revising the NEGF code, and may change the energy levels to be around the Fermi level. If you want to use NEGF, I recommend the latest development version of CP2K. And I will try to answer further questions.
Concerning your second question. It is the advantage of the NEGF approach that T(E) is changed with bias voltage. But as a simplest way to get I(V), the zero-voltage transmission can sometimes be used. Very carefully to make sense. It depends on the problem, of course. If the energy levels of the central system are not changed at finite voltage, one can omit self-consistency at finite voltage and use T_0(E).
Best wishes,
Dmitry Ryndyk