Why would food rot faster in the royal granary? more rats and bad locations?
And why would dukes be allowed to access the royal treasury?
It is mostly a balance thing I think, and as such a real world "reason" is not strictly required. In other words it exists to ensure that realms don't try to store massive amounts of food in the royal granary in order to completely circumvent regional markets.
One thing I have often thought about, Dukes have the ability to tax gold from their regions, but not food. Back when Dukes were always the lord of the city I often though it would be useful if they could set a tax rate on food as well. Given that Dukes no longer necessarily control the city some though about where the taxed food is stored would be necessary.
