Public End Date is the date displayed to applicants as the deadline for the opportunity. This date also dictates what questions, both Applicant and Administrator, will be displayed on the applications.
If a question is added AFTER the Public End Date of an opportunity, including questions added to the General or Conditional applications, those questions will not be displayed within the opportunities. The only way for that new question to propagate down to the ended opportunity is to move the public end date forward in time and essentially "reopen" the opportunity via the PUBLIC end date. Please note that the answers to these questions will not appear unless you also extend the INTERNAL end date as well.
Internal End Date is the date the system will stop automatically matching applicants to an auto-match opportunity regardless of the public end date. If there is no Internal End Date, the opportunity will continue to match applications until it is archived.
Once the Internal End Date has passed, all of the applications being displayed were qualified on that date and if an applicant becomes unqualified based on imported data later (should you allow for imported data to continue updating applications on those ended auto-match opportunities), the application will remain but the qualification points will be displayed as 0.
This also allows you to change the qualifications of an opportunity after the internal end date, but if the qualifications are updated after the Internal End Date, only qualified applications AS OF the Internal End Date will be displayed in the opportunity, meaning some of the previously qualified applications being displayed may be removed and new applications may appear.