Cleaning Contacts without adding onboarding group
The "clean contacts" functionality includes onboarding contacts as well. Ideally, these numbers would reflect the number of contacts who were sent the last X emails and did not open, not just did not open, which would include newly added contacts.
The 'Clean Contacts' function has limited customization, but that is not the only way to identify non-engaged users. For your scenario I would recommend using a Segment, which allows for much more specific instructions. You can filter for contacts who have been sent above a certain number of emails, or who have been in your above for longer than a period of time. I've listed below several built-in segment templates that would give you a great starting point. You can find these at Tables > Contacts > Segments > Segment Templates.
Non-Engaged Subscribers - No Opens in Last 50 Messages
Non-Engaged Subscribers - No Opens in Last 25 Messages
Non-Engaged Subscribers - No Activity for 6 Months
Non-Engaged Subscribers - No Activity for 12 Months
If you experience any issues with these segments, or would like assistance in customizing them to your needs, I would recommend opening a case with our Support Department.
Thanks so much, and have a good evening,
Jocelyn @ Bronto