As far as I can tell, this is no longer a problem. In particular, I have
a ~/.config/autostart/chromium-browser.desktop file with a timestamp
from 2017, and it is set to run Chromium normally (without --no-startup-
window).

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https://bugs.launchpad.net/bugs/1070823

Title:
  chromium-browser deletes modified autostart files

Status in chromium-browser package in Ubuntu:
  Incomplete

Bug description:
  Chromium does not have X session support; see
  http://code.google.com/p/chromium/issues/detail?id=23001

  However, if you configure it to run in the background, then it
  installs a ~/.config/autostart/ file. This combined with configuring
  to restore windows on startup would give effectively session
  management, but for one small problem: the autostart file is created
  with --no-startup-window. This makes sense, because the configuration
  item is to run Chromium in the background.

  However, if I then edit the command in gnome-session-properties, then
  on next startup, Chromium REMOVES the autostart file! This is bad
  behaviour: apps should not modify or remove configuration files once
  the user has edited them (for example, consider the management of
  configuration files under /etc when packages are upgraded).

  Hence, if Chromium were simply prevented from changing the autostart
  file if it is user-edited (i.e. has non-default contents), then it
  would be possible to get effective session management, even without
  explicit support for XSM.

  ProblemType: Bug
  DistroRelease: Ubuntu 12.10
  Package: chromium-browser 22.0.1229.94~r161065-0ubuntu1
  ProcVersionSignature: Ubuntu 3.5.0-17.28-generic 3.5.5
  Uname: Linux 3.5.0-17-generic x86_64
  ApportVersion: 2.6.1-0ubuntu3
  Architecture: amd64
  Date: Wed Oct 24 13:11:32 2012
  Desktop-Session:
   DESKTOP_SESSION = gnome
   XDG_CONFIG_DIRS = /etc/xdg/xdg-gnome:/home/rrt/local/etc/xdg:/etc/xdg
   XDG_DATA_DIRS = /usr/share/gnome:/usr/local/share/:/usr/share/
  DiskUsage:
   b'Filesystem     Type      Size  Used Avail Use% Mounted on\n/dev/sda1      
ext4      451G  149G  280G  35% /\nudev           devtmpfs  3.9G  4.0K  3.9G   
1% /dev\ntmpfs          tmpfs     1.6G  1.2M  1.6G   1% /run\nnone           
tmpfs     5.0M     0  5.0M   0% /run/lock\nnone           tmpfs     3.9G  3.0M  
3.9G   1% /run/shm\nnone           tmpfs     100M     0  100M   0% 
/run/user\ncgroup         tmpfs     3.9G     0  3.9G   0% /sys/fs/cgroup\n'
   
   Inodes:
   b'Filesystem     Inodes IUsed IFree IUse% Mounted on\n/dev/sda1         29M  
1.5M   28M    6% /\nudev             984K   606  984K    1% /dev\ntmpfs         
   987K   546  987K    1% /run\nnone             987K     2  987K    1% 
/run/lock\nnone             987K    15  987K    1% /run/shm\nnone             
987K     1  987K    1% /run/user\ncgroup           987K     9  987K    1% 
/sys/fs/cgroup\n'
  Env:
   MOZ_PLUGIN_PATH = None
   LD_LIBRARY_PATH = None
  InstallationMedia: Ubuntu 11.04 "Natty Narwhal" - Release amd64 (20110427.1)
  SourcePackage: chromium-browser
  UpgradeStatus: Upgraded to quantal on 2012-10-19 (4 days ago)
  chromium-default: CHROMIUM_FLAGS=""
  gconf-keys: /desktop/gnome/applications/browser/exec = 
b'/usr/bin/chromium-browser\n'/desktop/gnome/url-handlers/https/command = 
b'/usr/bin/chromium-browser --new-window 
%U\n'/desktop/gnome/url-handlers/https/enabled = 
b'false\n'/desktop/gnome/url-handlers/http/command = 
b'/usr/bin/chromium-browser --new-window 
%U\n'/desktop/gnome/url-handlers/http/enabled = 
b'false\n'/desktop/gnome/session/required_components/windowmanager = 
b'compiz\n'/apps/metacity/general/compositing_manager = 
b''/desktop/gnome/interface/icon_theme = 
b'gnome\n'/desktop/gnome/interface/gtk_theme = b'Clearlooks\n'

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