1. Why do you believe it is important to remove the root? Have you read http://blogs.telerik.com/fiddler/posts/13-08-19/faq---certificates-in-fiddler
to understand the security model for Fiddler certificates?
2. When you use the CertMaker addon, only
the root is added to the Windows certificate store (and only if you allow it). In contrast, the built-in certificate maker MUST put all server certificates in a Windows certificate store (as they're generated using the Windows certificate API).
If you want to trust the Fiddler root but also want to remove it every time you close Fiddler, you can do so using FiddlerScript. In the OnShutdown method, add
This will obviously make using Fiddler considerably less convenient.
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