weired issue with flycheck enabled

[tshu-w]

If I enable flycheck-mode, cache files will be saved to chemacs dir. here is an example init, with (setq native-comp-eln-load-path (list (concat user-emacs-directory "var/eln-cache/"))) in my early-init.el

(setq package-archives '(("melpa"        . "https://melpa.org/packages/")
                         ("melpa-stable" . "https://stable.melpa.org/packages/")
                         ("org"          . "https://orgmode.org/elpa/")
                         ("gnu"          . "https://elpa.gnu.org/packages/"))
      package-user-dir (concat user-emacs-directory "elpa/"
                               (format "%d%s%d"
                                       emacs-major-version
                                       version-separator
                                       emacs-minor-version)))

;; initialize packages
(unless (bound-and-true-p package--initialized) ; To avoid warnings in 27
  (setq package-enable-at-startup nil)          ; To prevent initializing twice
  (package-initialize))

;; setup `use-package'
(unless (package-installed-p 'use-package)
  (when (not package-archive-contents)
    (package-refresh-contents))
  (package-install 'use-package))

(require 'use-package)

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(use-package no-littering :ensure t :defer t)

; (use-package flycheck
;   :ensure t
;   :hook (prog-mode . flycheck-mode))

GNU Emacs 28.0.50 (build 1, x86_64-apple-darwin20.5.0, NS appkit-2022.50 Version 11.4 (Build 20F71)) of 2021-06-21

`etc` `var` and `eln-cache` was not generated in chemacs dir(`~/.emacs.d/`) without flycheck enable.