I'm testing out deploying the DesktopCentral agent via Intune to devices that going through the Autopilot process.  I created the intune win32 app file with the localagent directory and also created a install.cmd file with the following:

msiexec /i “DesktopCentralAgent.msi” TRANSFORMS=”DesktopCentralAgent.mst” ENABLESILENT=yes REBOOT=ReallySuppress /qn MSIRESTARTMANAGERCONTROL=Disable c:\InstallReader.log

During autopilot it will never advance past the DcAgent install.  When you go to intune you see it has failed: The unmonitored process is in progress, however it may timeout. (0x87D300C9)

I guess I should mention that we are using Secure Gateway and I'm hoping that the agent will register.