Please, pardon me, I've misunderstood your question.
To make things clear - there is no such option (neither in the registry nor anywhere else) where you can set the install path, so when you run the installer (either manually or through the auto-upgrade feature of Fiddler) it installs Fiddler to that location.
However, in your case you don't need that anyway. As long you have access to the command-line parameters of the installer you can set the install directory without going through the UI. You can specify the output path by passing it to the /D parameter. Example:
FiddlerSetup.exe /D=C:\Program Files (x86)\Fiddler
You should keep in mind few things:
1. This should be the last parameter used.
2. It must not contain any quotes, event if the path contains spaces.
3. The path given should be absolute path.
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