If this edge case bothers you a lot, then we could expand the rule so that you always get advantage against an unaware opponent, regardless if you can see it or not.
I think I would have to add that, personally. I see your point, believe me, but I also see the advantage is due to the opponent being unaware of the attack. Perhaps this is something more that having surprise would deal with?
At least if you are standing in the middle of a Fog Cloud and someone is shooting arrows into the cloud, you're going to be moving and aware of attacks, so I can see the attacker
not benefiting if they can't see you, either.
Bonus action for the Assassin to off-hand attack the Invisible Stalker with a light bag of flour (covering the Invisible Stalker on a hit). Followed by an action to attack with their shortsword and... sneak attack.
Need a bit of buy-in from the DM on the bonus action flour "attack". And hope that the airborne flour doesn't also create a heavily obscuring cloud...
Yeah, this would require some DM buy-in LOL!
First, technically you can't use your Bonus Action to Attack
until you have attacked with the Attack action.

It's a minor issue, but it means for this to work you would have to:
Attack with the bag of flour. It would be a ranged attack (with an improvised weapon) against the stalker's AC, similar to oil or holy water I would think.
Then use your bonus action for the second-weapon shortsword and sneak attack. The only downside to this method is no DEX mod to damage with the shortsword since it becomes your second-weapon. Again,
Unless you are using a 20-lb bag of flour, I doubt it would be enough for heavy obscurement!
