Units will still clump when in cover. Its the only way they can fit in cover.
Its a choice the player will have to make when facing the enemy. If there is a lot of AOE damage coming your way, you might not want to be in cover.
This is also true when facing flamethrower units. Your squads take much less damage when you stand outside cover because they don't clump up.
That sounds like now it should work like it is supposed too because AoE weapons like ARtillery and Mortars should deny diggin'-in-playstyle