Whether a model is in cover is never the end of the question when it comes to that model's unit receiving a cover save. Until you get to page 22, the cover rules are written with the assumption that the unit is entirely in cover. In Units partially in cover, on page 22, they add the next level of complexity - what if the entire unit is not in cover? At that point they say:
If half or more of the models in the target unit are in cover, then the entire unit is deemed to be in cover and all of its models may take cover saves. .... Of course being in cover or not often depends on the position of the firer as well as the target. If only one model is shooting, it will be easy to tell how many models in the target unit are in cover from the firer's point of view. If multiple models are shooting, you will need to work out how many models are in cover the point of view of the majority of the firing models that are in range. If the majority of the firers have a clear shot to the majority of the models in the target unit, the unit receives no save. Otherwise it does.
The only rule we have for shooting through units or area terrain is:
If a model fires through the gaps between some elements of area terrain ... or through the gaps between models in an intervening unit, the target is in cover, even if it is not completely visible to the firer.
The rules don't say that you receive a cover save simply because LOS goes through an intervening unit. In fact, the bottom diagram on page 23 makes it clear that shooting through units follows the 50%-to-50% rule: "The majority of unit B is in cover behind other models."