Not all attacks have splash. Cover could simply increase your elemental resist and dodge chance on direct projectile attacks coming from directions your covered against. They could easily reimplement physical resistance as well.
Splash attacks like fireball and grenades could be a way to get around cover, of course. Could be one of the advantages of magic.
Of course it's a big addition, requiring lots of rebalancing and changes to AI, so I wouldn't be surprised if it got scrapped. But I think it would be a unique addition to a fantasy RPG. I can't think of a pure fantasy RPG with cover. I don't think it should define the game like with shadowrun, but it's another tool for designing fights that encourages tactical maneuvering for flanking.
