It's more like äta upp means to eat to completion, but it doesn't really say that you're eating all of the food - just that you're eating all of what you're eating. So if you add the all as well, it means that not only are you eating of all the available food - you're also eating until there's nothing left of anything.
Just standard definite vs indefinite in Swedish here, actually. If you say maten, you're talking about some food specifically. But if you say mat, you're just talking about whatever food you have in general, so to speak.
In practice, these can be pretty interchangeable for the most part.
I think that would be Vem ät upp all mat. But "Who ate all the food" feels so much more natural that I keep making this mistake when I'm trying to go fast!
I suppose the context here could be that something keeps happening: "Someone always eats the food in the canteen before I get there! Well, who eats all the food?"
I would be much more likely to interpret this sentence in Swedish as e.g. "Who's that guy, eating all of our food?" - so the present tense is better in English as well. I agree the translation gets clunky, though. Changing the default might be a good idea - how do you feel about "Who is eating all of the food?"
It is, yes. The whole äta upp thing is problematic. It does imply completion - but it doesn't make it explicit. If English said e.g. "... eating all of the food", Swedish would translate that differently, into e.g. ... äter upp all maten. Neither way is really good here. It's an excellent example of a place where Duolingo would benefit from being able to show hints in relation to phrases or concepts.