You can create a Configuration Group based on the <File Version> of the msiexec.exe file itself. If you wish to find any computer that is not running version 3.1, try a rule similar to:
NOT <File Version> "%winsysdir%\msiexec.exe" MATCHES "3.1.*.*"
Simply create a new User Defined Configuration Group, click "Go to Editor", and paste in the above text. Give the rule a name like "NOT Version 3.1" and click Finish. For readability, you can rename the parent level group that gets created to "Msiexec Versions" (or something similar).
If you would like to check for specific versions, try the following groups:
<File Version> "%winsysdir%\msiexec.exe" = "2.0.2600.0"
<File Version> "%winsysdir%\msiexec.exe" = "2.0.2600.1183"
<File Version> "%winsysdir%\msiexec.exe" = "3.0.3790.2180"
<File Version> "%winsysdir%\msiexec.exe" = "3.1.4000.1823"