After customizing my MST file using the Adobe Customization Wizzard DC, i used this command line in SCCM 2012 to deploy as an Application.
msiexec /i "AcroPro.msi" TRANSFORMS="myMSTfilename.mst" /q
With previous versions, i had issues installing with Microsoft Outlook open but with this version (DC), SCCM simply did a popup message saying a reboot is required to complete the installation.
In my MST file i specified the following items:
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