Your understanding is correct. Because the work is major, including midweeks, approval has been made to offer refunds. It can’t be done via the live system because that only gets updated every 4 months. You may remember that while London Bridge was being rebuilt a few years back there were changes to the live fares because the overall duration of the relevant phases was significant enough to make a change. Southeastern probably had to pay TfL to account for lost revenue on journeys that were not forced by the works.
Whilst I’d love to be proved wrong, I don’t see the fact that refunds are being considered for this work as an indicator that they might always be available. Indeed Charing Cross and Waterloo East were closed last Sunday in preparation and there were no refunds available then.