It's not really two different two-probe "models" - the calculations are performed exactly the same way. It's simply different physical systems to model: in the first case, it's a heterojunction (single interface) between a metal and a molecular crystal (not quite a semiconductor), in the second it's also a heterojunction but now between two doped semiconductors. And, in your picture it's a metal-semiconductor-metal structure, although the semiconductor in this case is more like a large molecule, but that's also fine.
This is, you can say, one of the strengths of ATK - you model what you want to model. You can study different physical setups and configurations, which are relatively close to the experimental "reality", without making too many of the traditional assumption (slab model, no doping, etc). If you want to model a doped system like a p-n junction you do that, if you want to know the properties of a heterojunction you set up such a system, if it's a M-S-M system that you are trying to understand, as in your picture, then you choose that.