First of all, we are perhaps talking about two different things. I initially understood the question as related using the Berry phase to compute the polarization of a piezoelectric material. Here, the feature exists in ATK but is not well tested, and also exists in Abinit and you can find many publications on such calculations.
But the ferroelectric junction calculation you refer to is not related to that, but is a more normal transport calculation, of a type that can definitely be carried out in ATK, and does not require any new features implemented lately. In fact, there are at least 4 articles of similar nature to the one you mention, and which are based on ATK:
DOI:10.1063/1.3462070
DOI:10.1021/nn1031438
DOI:10.1103/PhysRevB.85.064105
DOI:10.1063/1.3698503
You could in principle use Abinit in the same way Tsymbal et al. used VASP, but in that case it's only possible to get a rough estimate of the transport properties, whereas with ATK you can truly compute them.
As you can see from all these articles, the electric states are not really something you set in the calculation as a parameter (like the spin for magnetic tunnel junctions) but rather a consequence of the internal polarization arising from small asymmetries or charge transfer at the surface to the electrodes. Specifically, the paraelectric (PE) or non-ferroelectric state (NFE) is obtained by a geometry optimization at zero bias, and the ferroelectric state (FE) by an optimization at a small electric field.
I find the discussion in PRB 85, 064105 (2012) (one of the articles in the list above) particularly enlightening and very detailed.