Administrative Installation: As Phil says, we wonder what you really want to achieve? If you just want to figure out what files are different inside the two setups, then I would use an administrative installation for each MSI (essentially a file extraction for the MSI - shorter explanation) and then use a file / folder-comparison software to check what files are different. My favorite tool for this is Beyond Compare (no affiliation, screenshots), but any file / folder comparison tool will do.
Running an administrative installation from a cmd.exe:
Option 1, interactively: msiexec.exe /a File.msi
Option 2, silently: msiexec.exe /a File.msi TARGETDIR=C:\MyInstallPoint /qn
Dark.exe: You can also use WiX's aptly named Dark.exe
to decompile an MSI - regardless of what tool was used to make it - into its constituent parts and the associated WiX markup needed to compile it again (needs some black art to clean up).
To extract contents from the MSI, you can try this command line:
dark.exe Setup.msi -x Files
Though likely flattened (without folder structure) you should be able to compare the files extracted from the setups using Beyond Compare as described above.