Just to expand on this: NPC's can use gap closers (charge/grapple) on PC's in cover. The reverse is not true. So apparently the way cover is coded currently is that players can't use gap closers on targets in cover, not that targets in cover are immune to gap closers (a subtle but important distinction). Either allow us to charge/grapple mobs in cover, or make it so mobs can't charge/grapple us if we're in cover.
Good call. It makes sense from a technical standpoint, too; it's easier to make a charge/grapple ability check if the target is in cover when the player attempts to use the ability as opposed to making the Crouch/Take Cover buff check to see if any enemies are currently trying to charge/grapple you and prevent them from doing so.
That said, mob charges and pulls need to respect cover.