Just create a transform manually. The only thing in the transform should be to install mms.cfg to the correct location. The mms.cfg file will contain the settings for the updates.
My problem right now is that 126.96.36.199 does not seem to grey out the 'change update settings' and 'Check Now' buttons with 'AutoUpdateDisable=1' in the mms.cfg file.
I had to do this in two parts. Firstly I deployed the MSI of 188.8.131.52.
Then I created a startup script .bat file for the computers being deployed to which contained the following:
xcopy "\\server\software\Adobe\Flash 11\mms.cfg" "C:\WINDOWS\System32\Macromed\Flash\" /o /y
xcopy "\\server\software\Adobe\Flash 11\mms.cfg" "C:\Windows\SysWOW64\Macromed\Flash\" /o /y
The mms.cfg that is copied to the local machines contains the following:
This seems to work as I have checked the machines deployed to as they now look like this: