"Format-specific differences" warning can be confusing
A FreeBSD developer compared two hybrid ISO+MBR images, and received the "Format-specific differences" warning:
Format-specific differences are supported for this file format but none were detected (DOS/MBR boot sector; partition 1 : ID=0xee, start-CHS (0x0,0,2), end-CHS (0x3ff,255,63), startsector 1, 673927 sectors)
(Sadly, FreeBSD's pkg collection has Diffoscope 103 so doesn't have the most recent version of this message, but the issue exists in both.)
I believe that these images are correctly detected as iso9660 and compared using isoinfo, but when no differences are found from that the file/libmagic string is emitted in the warning. This gives the impression that these files were compared as DOS/MBR boot sectors, not ISO images.