Newer nixpkgs has test files pkgs/test/make-binary-wrapper/overlength-strings.* with Nix store paths that are very long on purpose. fc-userscan should probably just emit a warning instead of failing when trying to register them as GC root. The error message is also a bit misleading as it doesn't show the problematic source file that contains the path:
ERROR: Create(
"/nix/var/nix/gcroots/per-user/x/home/x/nixpkgs.23.11/pkgs/test/make-binary-wrapper/00000000000000000000000000000000",
Os {
code: 36,
kind: InvalidFilename,
message: "File name too long",
},
)