Identified what commit is most probably the root cause:
https://github.com/uutils/coreutils/commit/37c42a29caa9f20a7d509cf59b9f3d177075aa5c

Essentially upstream changed the nix crate to rustix which makes id use
a raw syscall rather than the libc wrapper with getuid(). fakeroot
intercepts libc's function calls using LD_PRELOAD, but this gets
circumvented by the raw syscall.

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https://bugs.launchpad.net/bugs/2160614

Title:
  id: fakeroot does not fake root (regression: 0.8.0 -> 0.9.0)

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