Looks like you can...
Edit the "iTerm Rosetta/Contents/Info.plist"; updating the following section, from:
<key>CFBundleIdentifier</key>
<string>com.googlecode.iterm2</string>
To something like:
<key>CFBundleIdentifier</key>
<string>com.googlecode.iterm2rosetta</string>
If you then run "iTerm Rosetta" it will crash due to the above file no longer matching the app's signature.
You can get past that issue by renaming the "_CodeSignature" file in the "iTerm Rosetta/Contents" folder to something else, e.g. "ORIGINAL_CodeSignature".
Running "iTerm Rosetta" should now should now be successful.
With the new identifier set; "iTerm Rosetta"'s configuration is taken from "~/Library/Preferences/com.googlecode.iterm2rosetta.plist" — giving you the separation you desire.
Of course, you're dropping a security control with the above hack... Up to you as to whether that is acceptable to you or not.
Cheers,
aid