Give the teams a chance to run the tanks to 1ml and it'll get crazy with cars stopping on the last and slowdown laps when they get it wrong. The 1L thing means there is reserve for them to drive it home and only stop if they think they're in trouble, rather than because they actually are. As the FIA said, they take into account the inlap for their calculations, so if 1.7L came out but say, the inlap that wasn't completed would have used 0.8L extra, then you can see why it fails.
Formula E has a maximum power usage rather than running the batteries flat for the same reason. You don't actually want the teams to run out of juice across the line regularly and be unable to get back to the pits.
With 1L, there is plenty of space for impurities to be diluted enough so that any fouling or a couple of loose "illegal bits" can be measured without massively distorting it. One fleck of something that's 1ppm in a litre is likely to be many more ppm in a ml, which could fail it. With a litre, it gives the fuel a chance to mix and allow outliers and specific areas of concern to massively distort a reading. The illegal bit of fuel may have disappeared by the time you're down to 1ml of the other, less dense fuel which floated on top.
Rules are rules and 1L is not a difficult thing to produce or store in a car.