In TimeXtender Classic you can have as many Datawarehouses as you want and move data between them. While you can add many Data Areas inside one instance in TDI, you cannot have data move from one Prepare Instance to another.
The main advantage to this is that each Prepare Instance can be its own, appropriately scaled, infrastructural entity. One example is the situation where you have an implementation that starts growing horizontally: adding more subcompanies to a group, or adding more data due to acquisitions. In this case your database might not be scalable to handle the new data, or the project might be getting too large.
In this case instead of scaling up a huge database to be able to handle the peak load, you can split out into smaller chunks. This also allows separating out HR data into separate hardware.