Версия: gpupdate-0.13.2-alt1

Поскольку ключи прилетают, а /etc/gpupdate/environment и .gpupdate_environment настроены, то всё выглядит так, будто /etc/pam.d/system-policy-gpupdate - кривой.

#%PAM-1.0
session         [success=2 perm_denied=ignore default=die]      pam_localuser.so
session         substack        gpupdate-remote-policy
session         [default=1]     pam_permit.so
session         [default=7]     pam_permit.so
session         [success=1 default=ignore]      pam_succeed_if.so user ingroup users quiet
session         [default=5]     pam_permit.so
session         [success=1 default=ignore]      pam_succeed_if.so uid >= 500 quiet
session         [default=3]     pam_permit.so
session         [success=1 default=ignore]      pam_succeed_if.so service = systemd-user quiet
-session        required        pam_oddjob_gpupdate.so
session         optional        pam_env.so user_readenv=1 conffile=/etc/gpupdate/environment user_envfile=.gpupdate_environment
session         required        pam_permit.so

Как минимум, pam_env.so настроен не по man'у:
OPTIONS
       conffile=/path/to/pam_env.conf
           Indicate an alternative pam_env.conf style configuration file to override the default. This can be useful when different services need different environments.

       debug
           A lot of debug information is printed with syslog(3).

       envfile=/path/to/environment
           Indicate an alternative environment file to override the default. The syntax are simple KEY=VAL pairs on separate lines. The export instruction can be
           specified for bash compatibility, but will be ignored. This can be useful when different services need different environments.

       readenv=0|1
           Turns on or off the reading of the file specified by envfile (0 is off, 1 is on). By default this option is on.

       user_envfile=filename
           Indicate an alternative .pam_environment file to override the default. The syntax is the same as for /etc/security/pam_env.conf. The filename is relative to
           the user home directory. This can be useful when different services need different environments.

       user_readenv=0|1
           Turns on or off the reading of the user specific environment file. 0 is off, 1 is on. By default this option is off as user supplied environment variables in
           the PAM environment could affect behavior of subsequent modules in the stack without the consent of the system administrator.

           Due to problematic security this functionality is deprecated since the 1.5.0 version and will be removed completely at some point in the future.

FILES
       /etc/security/pam_env.conf
           Default configuration file

       /etc/environment
           Default environment file

       $HOME/.pam_environment
           User specific environment file


Сейчас в исходниках /etc/gpupdate/environment настраивается аналогично .gpupdate_environment, хотя там синтаксис должен быть как в /etc/environment (KEY="VAL").
Если в /etc/gpupdate/environment привести синтаксис в порядок, а после в /etc/pam.d/lightdm для Workstation K или /etc/pam.d/lightdm для GNOME добавить -session        required        pam_env.so envfile=/etc/gpupdate/environment readenv=1 - то переменные будут получены.

Также, хочу упомянуть о использовании pam_env.so и проблемах с переменными, определёнными в /etc/profile - https://bugzilla.altlinux.org/53948

(Ответ для Vladislav Glinkin на комментарий #1)
> или /etc/pam.d/lightdm для GNOME

/etc/pam.d/gdm-password*

gpupdate-0.14.0-alt1

Проблема не воспроизводится, переменные окружения успешно создаются и удаляются. Воспроизводится поведение из #51016#c14, т.е. теперь ситуация одинакова для DC на Windows и на Alt Server.
Данную ошибку закрываю.