Adobe's only officially supported method of installation of Adobe Flash Player on OS X clients is via the installer application bundle in the Install Flash Player .dmg file.

Installation via the extracted pkg from within the application bundle does not update the Adobe Flash Player Installer Manager application located in /Applications/Utilities if it already exists, which can cause issues with inventory and reporting of an otherwise successful managed installation.

You can successfully deploy Flash Player for Mac clients using the Adobe's preffered method with a little tweaking of the application bundle:

• Copy Adobe Flash Player Installer.app from the installer .dmg to writeable media/volume (Desktop in my example) 
   
• Edit the info.plist file in the Adobe Flash Player Installer.app to not show a dock item with the following commands:

defaults write ~/Desktop/Install\ Adobe\ Flash\ Player.app/Contents/Info LSUIElement -int 1
chmod ugo+r ~/Desktop/Install\ Adobe\ Flash\ Player.app/Contents/Info.plist

• Zip the edited Adobe Flash Player Installer.app and add as a Software Inventory Item
   
• Create a Managed Installation
   
• Configure Manually
   
• In order to allow installation without a logged in user, use the following Installation Command (all one line):
  
  

   

  sudo ditto -x -k -v --rsrc ./Install\ Adobe\ Flash\ Player.app.zip . ; sudo launchctl bsexec `sudo ps axwww | grep [l]oginwindow | awk '{ print $1 }'` ./Install\ Adobe\ Flash\ Player.app/Contents/MacOS/Adobe\ Flash\ Player\ Install\ Manager -install

-- edit 2013-07-30 15:42:18

To make managing the ongoing updates of the installer, I've simplified this to just use the original dmg from Adobe.  This way, you don't have to bother with editing the files and only need to zip the dmg and replace the attached file on the Managed Install.

• Download Install_Flash_Player.dmg from Adobe
• zip Install Flash Player.dmg and attach Install Flash Player.dmg.zip to Managed Install
• Use the following installation command:
  
  

  sudo unzip ./install_flash_player_11_osx.dmg.zip && sudo hdiutil mount ./install_flash_player_11_osx.dmg -nobrowse && sudo ditto -V /Volumes/Flash\ Player/ /tmp && sudo hdiutil unmount /Volumes/Flash\ Player/ && sudo defaults write /tmp/Install\ Adobe\ Flash\ Player.app/Contents/Info LSUIElement -int 1 && sudo chmod ugo+r /tmp/Install\ Adobe\ Flash\ Player.app/Contents/Info.plist && sudo launchctl bsexec `sudo ps axwww | grep [l]oginwindow | awk '{ print $1 }'` /tmp/Install\ Adobe\ Flash\ Player.app/Contents/MacOS/Adobe\ Flash\ Player\ Install\ Manager -install

What this command does:

unzip dmg
mount dmg silently
copies the embedded .app file to system temp directory
unmounts dmg
edits the Application properies to run as an agent so it does not create a dock icon, and makes the file readable by all users
use launchd to execute the installer using bootstrap context of loginwindow in order to be able to run without needing a logged in user