Hi mlrtime. You could run it on a base system, and use --exclude-path and --include-path all you want, to capture or ignore the things you don't care about.
Treat that as your 'golden' harvest state. You could then run a 'harvest' on the production system. You'd then be able to run 'enroll diff --old baseline --new production' to compare the difference.
You could also first run the manifest of the baseline harvest against your production, to ensure it has (at least) all the same things as the baseline.
A 'harvest' of production after that, would probably then show just stuff that existed on production already that wasn't in the baseline.
I hope that makes sense!