Jennifer,
This is quite a complex posting. After reading through, I like where it is going. Your proposal is if a certain version of a CAD file is associated to multiple versions of WTPart, then only build the latest version of the WTPart - don't build all versions of the WTPart. Yeah, certainly. That old A.10 WIDGET is old news.
I agree with Gregory Perasso. It would be very nice to make this a preference if possible. It probably doesn't need to resolve down to container level, but at least down to organization level. Maybe that is the core question: The change will be made...but does it need to be controlled by a preference for companies that don't want this functionality...or just force it?
My vote is preference-controlled function, default setting=No. This can be turned on to give the desired functionality in the supplied use-cases. (Or maybe in digging further, it is okay to set to Yes as default value?)