While I understand that Nix flakes are technically still "experimental", IMHO at this point it makes sense to enable them by default.
As per e.g. https://github.com/vorburger/nixfiles/blob/develop/docs/docs/reference/nix-cli.md (and similarly much elsewhere around the Internets), IMHO doing something like this during setup would ease the initial user experience:
echo "experimental-features = nix-command flakes" >> ~/.config/nix/nix.conf