We also have problems with the substitution of components in Pads Logic. We are trying to sustitute different components with different values from the same library in Pads Logic 9.5. When creating the BOMs, we have all different kinds of errors in these parts. Most of the times, we get the correct name of the substituted components, but the describtions and other attribures are from the "original" component. In some cases, the Substitution works. In the Lib, the attributes are correctly set for the substituted components.
To us the seems like a bug in Pads 9.5
looking forward for any good tips.
If you feel it is a bug you can raise a service request and inform mentor.
In the mean time i can suggest a workaround, you can place both the parts in the schematic and in the layout just overlap the two components and leave a note in assembly drawing saying for Assembly A mount X Component and for Assembly B mount Y component.