I don't think suggestions from Rene cam through so I will try in my own words:
You can use your own environment variables which hold the path to your own libraries. This will probably require you to change how your libraries are set up.
Anyhow using your own enviroment variables such as:
ROGER_CLARK_3D_MOD and ROGER_CLARK_MOD you can setup your own libraries and fp-lib-table entries. The fp-lib table entries should use ROGER_CLARK_MOD to point to the modules library while each module should use ROGER_CLARK_3D_MOD to point to its own 3D file.
This setup makes your module and 3D module library completely portable (for everybody who does not use the same environment variables for different purpose), so when you share the project you can share the library and person on receiving side should be able to use 3D files without any modifications (modules are already cached within the pcb file).
If you do not whish to share complete library there is always an option to write a script which scans your PCB file for 3D file references, copies the files into subfolder within the project and replace the reference such that it uses KISYSPROJ enviroment variable. (hmm this looks like a job for an Action plugin)
Only symbols libraries are somewhat difficult to share as you need absolute path. But usually it is one file only, so this not a big issue. Until v5 resolves this.