I wasn't even focusing on my own mod, but on X-Com in general.
Yes, flanking works on nuCom, but like everything else, it does so due to completely abstract and arbitrary rules, not because of how the simulation is constructed. In fact, there is no simulation, just a set of rules like in a card game. It works more like Age of Wonders: Planetfall; but AoW:P is a game of a greater scale (operating on the level of whole squads), so it's less jarring.