I personally think that to hit modifiers make more sense for cover (both thematically and for game design), it makes cover meaningful regardless of armour/toughness.
For the OP: "visible to the attacker" is actually a very badly written rule. Does it mean "drawing line of sight from any part of the model" or does it mean "if the model was alive and on a battlefield then would it be able to see?". Considering how GW writes rules, I would think the latter. I would add that most people can't really see through a crowd, regarding units. The rule isn't clear enough to really say, but that is how I prefer to do it.
If my opponent wants to "shoot at spear tips" then I let it slide (and do the same), it's not worth an argument or not having a game though, but I approach that game with a much more "gamey" attitude.
The lack of clarity in all of GW's rules is a major issue and has really made me prefer other systems. It would resolve most of the "rule confusion" issues if GW just defined terms and used them consistently.