Any part that has a configuration that depends on where it is used is a tough PDM problem to resolve.
There are two ways I handle this.
On items that are simple I set the item to be flexible and then customize the assembled item using that flexibility. A typical example is a hinge - the opening angle is set to be flexible so that for each placement the hinge can be adapted. Windchill sees only one model and each assembly (or even multiple uses within the same assembly) can have a unique angle.
The limit to my patience is currently a motor with related capacitor which required the use of parameters to drive the location and orientation of a csys to locate and orient the capacitor remotely positioned from the motor. 6 degrees of freedom for the one component -> six parameters + six relations.
This becomes a problem when the amount of variation gets to be burdensome, so I would not use it to route a multi-branch electrical cable.
For more complex situations I create items that are of the form base-name_installed-assy. If there is more than one in a single assembly they would get a numeric suffix Therefore the item that has a unique configuration based on it's assembled location is named, in part, for that location. The file with just base-name is the undeformed/nominal geometry.
The Common name for all the variations can be the same and repeat regions can gather them to make a BOM with correct quantities.
As for regeneration - make sure the mass properties are calculated in the footer. I think if the mass properties relation happens first it is marked invalid when the external references are updated and is then recalculated. It's marking it invalid and then replacing the value that marks the part as modified.** When it's at the end it is simply calculated. Since nothing is marked as changed, the part isn't marked as modified.
**I have no access to source code - this is a description of what the software seems to do, not necessarily what the underlying process is.
