It is possible to distinguish an Enterprise MSI installation from an EXE installation, but it's not easy, and it's version specific.
The Enterprise MSI installation creates a GUID in the HKLM\Software\Microsoft\Windows\CurrentVersion\Uninstall key of the registry.
The specific GUIDs (for each version) can be obtained from the Installed Ruleset of the Enterprise MSI installer package in the Software Publishing\Google Packages node of the Patch Manager console.
e.g. v32.0.1700.107 will have {56B708CC-28A0-3CFC-A83B-BE70E5C4EA18}
and v32.0.1700.102 will have {BAD37831-C0F3-3976-934B-D53674DA2335}
