Bees does things at a lower level than just reflinking full files like dupremove (it dedups at the level of extents). Be sure to read the links in the "Recommended Reading" section, of the above link, to hopefully avoid issues.
duperemove has "--dedupe-options=partial" which also enables this, not just full extents.
the issue still is, that the data within the archive is not block aligned, thus preventing me from deduplicating them properly
https://github.com/Zygo/bees
Bees does things at a lower level than just reflinking full files like dupremove (it dedups at the level of extents). Be sure to read the links in the "Recommended Reading" section, of the above link, to hopefully avoid issues.