Hi,
There has unfortunately been a bug in the way QuantumATK calculated the transmission for a bulk configuration, which in some case could lead to wrong transmission values. This was solved in the 2019.12 version.
1) Concerning the comparison between DFT and extented Hückel, you cannot in general expect to get the same results. In the attached scripts, the device is calculated with Hückel, while the bulk configuration with DFT. Usually this will give different results, at least quantitatively different. There might be qualitative agreement. The use of force fields for the phonons is usually fine.
2) Yes, the electrode size can matter, also for a perfect device. You can use the "Electrode Validator" to the right of the LabFloor to validate if a certain bulk configuration is a valid electrode.
Regards,
Troels