Thanks for the link to mysysprep page. It states the following
To solve this problem, we have to look at how a Sysprep'ed image set up. During setup, Preinstallation Environment (PE) is loaded first, and then PE runs the command line at the Registry HKLM\SYSTEM\Setup\CmdLine to start the setup process. The command line for Mini-Setup is "setup.exe -newsetup -mini". What we can do is to change the command line to execute our own setup and then our own setup executes the original Setup.exe.
I guess what that means is
- run sysprep with the exit option selected (not reboot)
- update the registry with the path of your executable in HKLM\SYSTEM\Setup\CmdLine
I will test it later. Hopefully it is that simple.