BTRFS reflinks as an option alongside hardlinks, this deals with duplicate files in a smarter way that makes sure that changing one file won't effect the other, even though they are using the same physical disk space to store the duplicated file.
BTRFS checksums, which are stored in the file system and do not need to be manually calculated by Czkawka this would speed it up a fair bit.
BTRFS is also unofficially supported on Windows though WinBtrfs, though this issue is not intended for this, just figured that it might be worth nothing since this program works on Windows as well.
Add support for BTRFS features:
Docs on BTRFS Deduplication, other docs, wikipedia
BTRFS is also unofficially supported on Windows though WinBtrfs, though this issue is not intended for this, just figured that it might be worth nothing since this program works on Windows as well.