I'm using my usual init file with native-comp build of Emacs, and it
doesn't work, while in current master version it works just
fine. Packages seem to load correctly only if there are `:init' keyword
in `use-package' declaration. The below is example init file that I can
represent the problem with:

    (defvar package-archives)
    (setq package-archives
          '(("gnu" . "https://elpa.gnu.org/packages/")
            ("melpa" . "https://melpa.org/packages/")))

    (when (version= emacs-version "26.2")
      (defvar gnutls-algorithm-priority)
      (setq gnutls-algorithm-priority "NORMAL:-VERS-TLS1.3"))
    (package-initialize)

    (unless (package-installed-p 'use-package)
      (package-refresh-contents)
      (package-install 'use-package))

    (require 'use-package)
    (setq use-package-always-ensure t)

    (use-package company
      :bind (:map
             company-active-map
             ("TAB" . company-complete-common-or-cycle)
             ("<tab>" . company-complete-common-or-cycle)
             ("<S-Tab>" . company-select-previous)
             ("<backtab>" . company-select-previous)
             ("C-n" . company-select-next)
             ("C-p" . company-select-previous))
      :hook (after-init . global-company-mode)
      :config
      (setq company-require-match 'never
            company-minimum-prefix-length 2
            company-tooltip-align-annotations t
            company-frontends
'(company-pseudo-tooltip-unless-just-one-frontend
                                company-preview-frontend
                                company-echo-metadata-frontend)
            company-backends '(company-capf company-files)))

    (provide 'init)

With this init file, load Emacs and open `*scratch*' buffer. Company
mode should be loaded and active because of `:hook', but no
configurations are applied, e.g. `company-minimum-prefix-length' is `3',
and bindings are not defined. The very same init file can be loaded in
Emacs built from master and it will configure company properly.


In GNU Emacs 28.0.50 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.13,
cairo version 1.16.0)
 of 2020-04-15 built on toolbox
Repository revision: 208a11d3f0ede17b29da45c2491b703b6942a764
Repository branch: feature/native-comp
Windowing system distributor 'Fedora Project', version 11.0.12006000
System Description: Fedora 31 (Workstation Edition)

Recent messages:
For information about GNU Emacs and the GNU system, type C-h C-a.
Making completion list...
Quit [3 times]
funcall-interactively: End of buffer
Making completion list...

Configured using:
 'configure --with-nativecomp --prefix=/home/andreyorst/.local/emacs
 --bindir=/home/andreyorst/.local/bin'

Configured features:
XPM JPEG TIFF GIF PNG RSVG CAIRO SOUND DBUS GSETTINGS GLIB NOTIFY
INOTIFY LIBSELINUX GNUTLS LIBXML2 FREETYPE HARFBUZZ ZLIB
TOOLKIT_SCROLL_BARS GTK3 X11 XDBE XIM MODULES THREADS JSON PDUMPER LCMS2
GMP

Important settings:
  value of $LANG: en_US.UTF-8
  value of $XMODIFIERS: @im=ibus
  locale-coding-system: utf-8-unix

Major mode: Lisp Interaction

Minor modes in effect:
  global-company-mode: t
  company-mode: t
  override-global-mode: t
  tooltip-mode: t
  global-eldoc-mode: t
  eldoc-mode: t
  electric-indent-mode: t
  mouse-wheel-mode: t
  tool-bar-mode: t
  menu-bar-mode: t
  file-name-shadow-mode: t
  global-font-lock-mode: t
  font-lock-mode: t
  blink-cursor-mode: t
  auto-composition-mode: t
  auto-encryption-mode: t
  auto-compression-mode: t
  line-number-mode: t
  transient-mark-mode: t

Load-path shadows:
None found.

Features:
(shadow sort mail-extr emacsbug message rmc puny dired dired-loaddefs
format-spec rfc822 mml mml-sec epa derived epg epg-config gnus-util
rmail rmail-loaddefs text-property-search time-date mm-decode mm-bodies
mm-encode mail-parse rfc2231 mailabbrev gmm-utils mailheader sendmail
rfc2047 rfc2045 ietf-drums mm-util mail-prsvr mail-utils company-oddmuse
company-keywords company-etags etags fileloop generator xref project
ring company-gtags company-dabbrev-code company-dabbrev company-files
company-capf company-cmake company-xcode company-clang company-semantic
company-eclim company-template company-bbdb company edmacro kmacro pcase
init cl-extra help-mode use-package use-package-ensure
use-package-delight use-package-diminish use-package-bind-key bind-key
easy-mmode use-package-core finder-inf info package easymenu browse-url
url-handlers url-parse auth-source cl-seq eieio eieio-core cl-macs
eieio-loaddefs password-cache json subr-x map url-vars seq byte-opt gv
bytecomp byte-compile cconv cl-loaddefs cl-lib tooltip eldoc electric
uniquify ediff-hook vc-hooks lisp-float-type mwheel term/x-win x-win
term/common-win x-dnd tool-bar dnd fontset image regexp-opt fringe
tabulated-list replace newcomment text-mode elisp-mode lisp-mode
prog-mode register page tab-bar menu-bar rfn-eshadow isearch timer
select scroll-bar mouse jit-lock font-lock syntax facemenu font-core
term/tty-colors frame minibuffer cl-generic cham georgian utf-8-lang
misc-lang vietnamese tibetan thai tai-viet lao korean japanese eucjp-ms
cp51932 hebrew greek romanian slovak czech european ethiopic indian
cyrillic chinese composite charscript charprop case-table epa-hook
jka-cmpr-hook help simple abbrev obarray cl-preloaded nadvice loaddefs
button faces cus-face macroexp files text-properties overlay sha1 md5
base64 format env code-pages mule custom widget hashtable-print-readable
backquote threads dbusbind inotify lcms2 dynamic-setting
system-font-setting font-render-setting cairo move-toolbar gtk x-toolkit
x multi-tty make-network-process emacs)

Memory information:
((conses 16 218313 8591)
 (symbols 48 15381 1)
 (strings 32 75978 3165)
 (string-bytes 1 2116064)
 (vectors 16 21109)
 (vector-slots 8 327508 7598)
 (floats 8 44 40)
 (intervals 56 336 0)
 (buffers 992 12))

-- 
Best regards,
Andrey Orst