No, the two calculations are not really the same numerically. Physically yes, kind of, but the algorithms are very different. Just to start with, there is no diagonalization of the Hamiltonian in the NEGF method, and also there are contributions to the Hamiltonian (and thus energy) from the electrodes, so one cannot even say the number of atoms is strictly the same. I honestly don't think you will find much benefit from this analysis unless you plan to write your own NEGF code...
The details of the NEGF method we use are well documented and links can be found in the manual, at the top of
https://docs.quantumatk.com/manual/NEGFDevice.html, plus
https://doi.org/10.1088/1361-648X/ab4007.