Vinod,
You actually have an answer in your own mail: use Shrinkwrap Feature in pipinh / harness assembly to capture all required references form any required level of top assembly. Thisis exact reason why shrinkwrap feature was created for. You can control its dependency i.e. you can "freeze" it for a while, or keep associative to top assembly.
IN your piping / harness assembly, first thing create this shrinkrap feature. Use Subset to only include relevant external models in it. This is very powerful feature with many options. BY default it will collect solid surfaces of components in subset, so if you need datums - add them manually.
Now create your piping / harness and reference ONLY to this SW feature.
Next time you get your piping / harness assembly you will see that shape of reference modules, but you will not have them neither physically nor in BOM.
In top assembly, if surfaces of this SW feature make any trouble - just Hide it. If you want to hide it in top assembly but to keep visible in piping / harness assembly you may need to create a special part for this SW feature, and comtrol its visibility from top assembly through layers.
Hope this helps,
- Vlad