That is the part that baffles me. There might be an argument against when this becomes unsustainable (e.g. the number of bytes inside a file is actually smaller

That is the part that baffles me. There might be an argument against when this becomes unsustainable (e.g. the number of bytes inside a file is actually smaller than the number of bytes the metadata associated with that file takes) but that can be solved quite intuitively by making user pay for it (essentially they should be counted towards the same usage limits, if they aren't already?).