The DDT is intended to upgrade data structures, and you should be able to create a DDT package that 100% upgrades an existing structure. However, it may require that you create some pre or post execution scripts to ensure that there is not any "residue" out there.
If you do not take the time to work through an upgrade solution via the DDT right now, then you will always be creating scripts and it goes against the purpose of the DDT.
The problem is that you have some existing structures, and honestly I don't totally understand your environment or problem, but it sounds as though your current deployments are not consistent. If this is the case, whether using the DDT or scripts, you would have to take this into account.
We created the pre deployment scripts for this very purpose, to clean up a dirty environment prior to allowing the DDT to do its thing. The DDT will move tables from one file group into another. So if you have a table called Customers in FileGroupA in a deployed environment, and when you deploy with the DDT it is assigned to FileGroupB, the Customers table will be moved into FileGroupB.
I hope that makes sense as I do not totally understand your problem and what types of environments and issues you are dealing with.