This is for EBS or Fusion Applications?
Moving this to EBS Community.
You are absolutely right that both the processes i.e. Inter-Org Transfer and the IRISO process are used to transfer the material from one org to another and the Inter-Org Transfer is an easy approach to perform this operation.
But the main reason why IRISO process is preferred over Inter-Org approach is that IRISO is a controlled process with proper request being initiated by the destination org (The org to which the items will be transferred) in the form of internal requisition which would then be converted into Internal Sales Order (ISO) and the order would be imported by the source org (The org which is going to transfer the items as per the request from destination org).
This way, the system will ensure that everything is under control and process driven which enables keeping a track during the flow of this process at any point in time. And most importantly this can be achieved automatically through inventory planning methods like Min-Max or Kanban planning with the source type as Inventory or Inter-Org respectively.
Whereas the Inter-Org transfer is not a controlled process. It just transfers the material from one org to another without any documents reference in the system.