At present, Fiddler's AutoSave feature isn't designed for unattended use, although that's an interesting option. I'd definitely be interested in learning more about your scenario, as there are a lot of really cool possibilities.
In the next build (Fiddler 22.214.171.124+) you can use
prefs set fiddler.extensions.AutoSave.AlwaysOn True
... in the QuickExec box to tell the AutoSave feature to automatically enable itself as Fiddler starts up.
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