Using custom-set-variables programmatically

How advisable is to use custom-set-variables programmatically within one's init file?

For example,

(custom-set-variables
 '(backup-directory-alist `((".*" . ,(concat user-emacs-directory "backup"))))
 '(tramp-backup-directory-alist backup-directory-alist)
 '(auto-save-file-name-transforms (append auto-save-file-name-transforms
				                          `((".*" ,(concat user-emacs-directory "auto-save") t)))))

This works as intended, but I am not sure if it is fine to do it. I prefer to set variables defined via defcustom this way for two reasons: customization types (https://www.gnu.org/software/emacs/manual/html_node/elisp/Customization-Types.html) and setters.