Debconf executes scripts from /tmp by default but you can try continuing 
securing the system by changing apt's temp file configuration:
https://serverfault.com/questions/72356/how-useful-is-mounting-tmp-noexec

Anyway this is definitely not a bug in u-u, maybe a wishlist one for
debconf.

** Changed in: unattended-upgrades (Ubuntu)
   Importance: Low => Wishlist

** Package changed: unattended-upgrades (Ubuntu) => debconf (Ubuntu)

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https://bugs.launchpad.net/bugs/1642863

Title:
  Upgrading unattended-upgrades gives errors and a warning

Status in debconf package in Ubuntu:
  Confirmed

Bug description:
  Ubuntu release
  ==============

  Description:  Ubuntu 16.04.1 LTS
  Release:      16.04

  Package version
  ===============

  unattended-upgrades:
    Installed: 0.90ubuntu0.2
    Candidate: 0.90ubuntu0.2
    Version table:
   *** 0.90ubuntu0.2 500
          500 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 
Packages
          500 http://archive.ubuntu.com/ubuntu xenial-updates/main i386 Packages
          100 /var/lib/dpkg/status
       0.90 500
          500 http://archive.ubuntu.com/ubuntu xenial/main amd64 Packages
          500 http://archive.ubuntu.com/ubuntu xenial/main i386 Packages

  What I expected to happen
  =========================

  No error or warning messages during a software upgrade.

  What happened instead
  =====================

  When an updated version of unattended-upgrades is installed, the
  following error messages appear because /tmp is mounted noexec for
  security reasons (see the Securing Debian Manual, section 4.10 at
  https://www.debian.org/doc/manuals/securing-debian-
  howto/ch4.en.html#s4.10):

      Preconfiguring packages ...
      Can't exec "/tmp/unattended-upgrades.config.5svL0F": Permission denied at 
/usr/share/perl/5.22/IPC/Open3.pm line 178.
      open2: exec of /tmp/unattended-upgrades.config.5svL0F configure 
0.90ubuntu0.1 failed at /usr/share/perl5/Debconf/ConfModule.pm line 59.

  Also, the following warning occurs later on:

      Setting up unattended-upgrades (0.90ubuntu0.2) ...
      update-rc.d: warning: start and stop actions are no longer supported; 
falling back to defaults

  ProblemType: Bug
  DistroRelease: Ubuntu 16.04
  Package: unattended-upgrades 0.90ubuntu0.2
  ProcVersionSignature: Ubuntu 4.4.0-47.68-generic 4.4.24
  Uname: Linux 4.4.0-47-generic x86_64
  ApportVersion: 2.20.1-0ubuntu2.1
  Architecture: amd64
  CurrentDesktop: Unity
  Date: Fri Nov 18 02:36:54 2016
  DistributionChannelDescriptor:
   # This is a distribution channel descriptor
   # For more information see 
http://wiki.ubuntu.com/DistributionChannelDescriptor
   canonical-oem-somerville-xenial-amd64-20160624-2
  EcryptfsInUse: Yes
  InstallationDate: Installed on 2016-11-01 (17 days ago)
  InstallationMedia: Ubuntu 16.04 "Xenial" - Build amd64 LIVE Binary 
20160624-10:47
  PackageArchitecture: all
  SourcePackage: unattended-upgrades
  UpgradeStatus: No upgrade log present (probably fresh install)
  modified.conffile..etc.apt.apt.conf.d.10periodic:
   APT::Periodic::Update-Package-Lists "0";
   APT::Periodic::Download-Upgradeable-Packages "0";
   APT::Periodic::AutocleanInterval "0";
   APT::Periodic::Unattended-Upgrade "1";
  mtime.conffile..etc.apt.apt.conf.d.10periodic: 2016-11-07T13:58:08.805628

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