If my understanding is correct, the problem with the qty is that one of the global warehouses they delivery to (Austraiia in this instance) has a different qty requirement to every other Country within the organisation and as such, changing the rounding qty in the MMR would have a greater negative impact.
With regard to short picking, you are of course correct in terms of short picks due to stock imbalances however, this requirement is for a known and accepted Global variance and as long as you assign a specific difference indicator outside of the default 'blank' (so that the picker has to consciously 'log' that it is a 'variance pick', thus making the picker accountable) this is an acceptable solution in terms of process and audit.
Cheers
A