...and don't forget the fact that, with a turn- and square-tile-based "combat sim", everything is an abstraction at some level...and something like cover is deeply abstract. Just because Xenonauts 2 is using a 3D graphics engine doesn't mean that it suddenly can, or even should, become more "realistic" than Xenonauts 1 was; just because you think you can see an alien's body better from one angle than from another doesn't mean that, in the meta-game, that alien can't duck behind that heavy cover to get the 50% bonus, or is so much behind the lighter cover that no matter how your soldier might be aiming they're still at a 30% penalty.
Now, that thought does pose a question/idea: why not create "dodge" animations for mobs - possibly just three each ("step to the left, step to the right, hunker down in place" - and that last could be a quick up-and-down of the crouch position, even), and have them use whichever is appropriate by having the shots pathfinding splitting the highest-level intervening cover object into 3 quadrants and, based on which quadrant the shot passes through as a straight mid-square to mid-square line, does the appropriate animation to indicate that the target is "making use of the cover?" That's a pretty simplistic description for the idea, but hey, "abstractions", right?