The comparison is with WordPress.org, not with us.
WordPress.org publishes checksums for the core files of every version. Those are exactly what Kakapo Security uses — not a list of its own that could go stale. If a file deviates, it is reported.
Checksums straight from WordPress.org · No comparison list of our own
The kakapo fetches the checksums
Every core file is compared
Deviations end up in the report
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