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Exiftool
mat2 is in fact using exiftool to extract metadata from files, but not to remove them. The previous iteration of mat2, MAT, was using exiftool to remove metadata, which lead to several cases where they weren't correctly removed, if at all. For example, Exiftool's documentation states the following with regard to PDF:
All metadata edits are reversible. While this would normally be considered an advantage, it is a potential security problem because old information is never actually deleted from the file.
To remove metadata, mat2 usually re-render the file completely, eliminating
all possible original metadata. See the implementation_notes.md file for
details.
jpegoptim, optipng, …
While designed to reduce as much as possible the size of pictures, those software can be used to remove metadata. They usually have very good support for a single picture format, and can be used in place of mat2 for them.
PDF Redact Tools
PDF Redact Tools is a software developed by the people from First Look Media, the entity behind, amongst other things, The Intercept.
The tool uses roughly the same approach than mat2 to deal with PDF, which is unfortunately the only fileformat that it does support. It's interesting to note that it has counter-measures against yellow dots, a capacity that mat2 doesn't possess yet.
Exiv2
Exiv2 was considered for mat2, but it currently misses a lot of metadata
Others non open source software/online service
There are a lot of closed-source software and online service claiming to remove metadata from your files, but since there is no way to actually verify that they're effectively removing them, let alone adding unique markers, they shouldn't be used.