The MPAA and other organizations use screenshots that show copyrighted material as "proof" that the tools are used for copyright violation, and then DMCA them.

If you want to help pay for lawyers to fight those DMCA notices with counterclaims and lawsuits, put up or shut up; the FSF, EFF and ACLU have been noticeably disinterested in doing so.

This has nothing whatsoever to do with fair use.

It's about arguments in court about the intention of the software if sued. Images of copyrighted content indicate intent to infringe copyright. Without those, you can argue it's only meant to find and index Linux image torrents or whatever.

Fair use doesn't enter the picture at all.