Thank you for your detailed post and reporting this bug to Apple. I'm having the exact same problem, but with DocumentGroup (instead of WindowGroup).
This bug seems to disappear when the .searchable modifier is used. See: https://stackoverflow.com/questions/69201709/focusedscenevalue-fixed-by-searchable
Using macOS 12.0.1 with Xcode 13.1 as well.
omar_a
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I'm having the same problem. This bug is also described in another post: SwiftUI and focusedSceneValue on macOS, what am I doing wrong?