thank you for the extra information.
what you showed in the screenshot is the dialog box we expected. I don’t know why it would take 3-5 minutes for the dialog to go away. That would be a macOS issue. We’ll research it.
The point of this new feature is that users need not manually invoke Hook in order to tell whether the current item has been hooked to something. Every time you switch to an app, Hook tries to see if it’s current item is hooked. macOS needs to request permission for every app that you bring to the foreground before Hook can communicate with it. (Apple does not provide a blank “allow Hook to work across apps”.) All Hook needs to do is get the number of links if the app is supported. We’ll revisit whether we can exclude a bunch of apps, keeping in mind that Hook works with many apps by default without Hook having a specific script for them and there are many apps out there.
If the feature is too annoying, we recommend turning off the feature from Hook’s general preferences or command line. If for some reason it is not sticking, try toggling “unchecked, checked, unchecked” (though in our test it works and in public beta it worked).