I've been confused by this as well.
I think the answer is that "unstoppable" does not mean immune to CC. It means that CC will not prevent the champion from going through with the ability. However the CC and any associated damage still actually happens, just while and after the ability takes place.
So a Vayne can condemn a Jarvan while he ults her, he is unstoppable and thus will still land on top of her and create the arena, but will also take damage from condemn (and if within range of a wall, will be stunned while in the air and while landing). Likewise with Vi/Malphite/Hecarim and anyone else who may be unstoppable when using an ability.
It would be most noticeable when the stun is very long lasting so that it persists after the unstoppable action. E.g. a 3-second max range Ashe arrow on a Jarvan as he ults, since it's the shortest unstoppable time combined with the longest CC, it would appear as if the arrow hit him after landing even if it hit him in midair.