An obstacle offers a greater measure of protection against missile fire to models hiding behind it. If a firer is shooting at a model that is behind an obstacle and in base contact with it, the target model counts as in cover (of the appropriate type), regardless of how much of it is visible above the obstacle. We assume that the warrior takes shelter behind the obstacle. When firing against a unit, the majority of its models must be behind the obstacle in order to benefit from this additional protection.
Firing models that are themselves in base contact with an obstacle may ignore it for the purposes of line of sight, just as if the obstacle was not there – they will lean over it as they fire.