Same issue here. :(
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We're facing a very similar issue. We have a URLRepresentableIntent intent that opens a universal link. When it's fired from the ControlWidget, the link only opnes in Safari. But if I run the intent from the Shortcuts app, it works as expected: it opens the app and the app handles the link.
Reported here FB14844990
Have you guys @yqiang @NickYaw found any solution?