I know doing a full boolean merge would be too difficult, but why not just delete any faces that are completely hidden (ie. contained inside other meshes)? This could be an export toggle, and would greatly reduce the amount of geometry on many creations with minimal processing overhead. 

We've tried tackling this issue but so far haven't found a method that would produce satisfying results regarding quality and processing time.

OR !

Create your templates so that there are no hidden faces

this is difficult as it requires you to modularize very carefully from a finished template, I used google sketchup for this.

like this for 1920's style cars (sedan - 5 models / sport car - 1 model / truck - 1 model with 3 different cargos):

- base 1 model

- motor 4 models

-cabin 3 models

-trunk 2 models

-wheel 2 models

-stering 1 model

-hood 4 models

-bench 1 model

-doors 2 models

- floor 1 model

-barrel 1 model

boxes 2 models