I'm not sure I entirely understand your objective, but the problem of de-duping across all formats, including the PC98 ones, is always an issue.
I know you have used my Dimwit program, with what success I do not know. I have been working on it, and one aspect is you can set it to log the MD5 of the data portion of multiple disks by drag&drop - just set logging on. Not the whole disk - just the unpacked sector data ( which is mostly what you are trying to compare ).
Disclaimers - it is obviously a work-in-progress and might evidence bugs. It is also quite slow at .d88s as there is quite a lot of unpacking to do.
If you wish to try it again the current version is at
http://www.blackdiamond.co.za/slt/Dimwit.7zScreenshot at
http://www.blackdiamond.co.za/slt/Dimwit1.pngIf it would be useful to add a column in the .csv log output for the write-protect, I'm sure I could do that, or any other field off the header (but the disk name is likely to cause issues - anything and everything in there!)
Judging from the file spec I cannot see any way changing from 672 to 688 byte header could affect anything - I am sure it is quite safe.
I'm not sure if this helps. If Dimwit is not working for you I'd love to know why, and apologize for wasting your time. Or if you have any ideas for a helpful tool for this, please say so.