NixOS + Home Manager user here.

I run in an opt-in state config. / is tmpfs. /home is tmpfs. /boot and /nix are real filesystems. At boot, the EFI loader reads the configuration from /nix/persist/etc/nixos/flake.nix, symlinks all the programs and configs into / and /home, and startup proceeds as normal.

That means nothing persists across boots unless I add it to my config. Cruft doesn’t accumulate in hidden areas, it’s all in my config. That keeps things fast, makes management easier, and makes troubleshooting easier.