PDM is not the reason that problems will occur. It can handle the relationships of structure since the assembly conditions are not carried up to the PDM side of things.
The problem is in the CAD side.
What happens if one component that is referenced is changed and the mating reference is deleted?
What happens when you use that same component in multiple assemblies and then rename it when making a change?
Why create complex assembly conditions that MAY cause failures if you do something in the future without remembering what you did years ago?
What if you leave the company and some new guy has to work on your assembly?
There are methods for doing some of the sub-sub relations, but you need to understand them. Skeleton parts are good for providing the reference structure for component placement.
KISS - Keep It Simple and Smart
Thank you,
Ben H. Loosli
USEC, INC.