I found a rendering difference for a sample PDF between two Poppler utilities. SavaPage uses pdftoppm to create PNG images for PDF preview, and pdftocairo to repair invalid PDF. The PNG images are OK, but the repaired PDF handle z-ordering of text and annotation differently. I reported as Poppler Issue 735. I’ll keep you posted.
Some movement. Issue seems to be related to an earlier one reported in 2015. Still no prospect of a solution.