If I am understanding the question correctly I think this may be an option.
We use Esko plug-ins to run Preflighting of files in Illustrator. This gives us our minimum percentage bumps, our warnings to look at, any missing or embedded images to look into, etc... Then we use Esko's PowerTrapper to apply traps or chokes. We adjust our overprints. And after all of that is done, we drop that production file onto a proof with the die lines, perfs, and folds laid out.
So in your case, it might make more sense to make the blank template file first on one layer. Then turn that layer off. Then run the processing on a different art layer. Turn the die line layer back on and check if there are any concerns.
The whole thing can be done in Illustrator with only the Esko plug-ins adding extra functions to the graphic program you may already be familiar with.
