If a character is prone and in cover does an attacker get both the -2 for shooting a prone target as well as the extra armor from cover?
If so this causes some questions, like why is it harder to hit someone prone behind cover as opposed to someone just sticking their arms and head around cover? They will be exposing the same target area and the same amount of their body will be behind cover.
A possible solution would be that taking cover gives attackers -2 to hit at all times, regardless if the target is prone or not, but that will make cover a lot better, especially cover in terrain that already gives attackers a penalty. For example, a regular forest would give attackers -3.
Another solution might be that a character cannot take cover while prone, but that doesn't make a whole lot of logical sense either.