all this depends which paradigm you come from.
For me the ZW Multi-object file seems the easiest to work with EXCEPT when one decides to complicate life with PDM/PLM etc. where each file has a life of its own.
So I am expecting you to create all the objects used in a tool box including it’s assembly in one file.
When you have this sorted, Save As a different version and you retain everything in one action.
Variant generation then becomes a cinch. (That needs interpretation) .
When you change the assembly from say 2 side by side draws to 3 x 3 , you’d revise a version/copy of the 2x2 file so that the assembly was correct, the drawings dimension correctly, the new dividers assembled etc. Then all size variants are copies of these. Off course the more complete the file is to start with the less work to do to subsequent copies. e.g. Make sure all the drawings are done to final stage.
What ever incomplete work there is in a file, the more work you have to do when it is duplicated!
Re ‘packing’ associate files. ZW does that too. In fact when you get down to it there is little that ZW does not already do. Although one needs to know you can do in order to know that.