When you are setting up Shipping Network, two options are available:
In the case of Direct, when inter org transfer is done, quantity of sending org is reduced and receiving org is increased without requirement of any further action.
In case of intransit shipment, it is a two step process. Receiving org need to receive the intransit shipment.
In transit shipment is useful when your inventory org is located in two different physical locations or when you need to have responsibility accounting for different orgs.