I'm afraid it's a bug in WebView2. We can work around it, but the workaround would break the Steam in-game overlay, which is important to commercial titles on Steam. So for now we're hoping that Microsoft fix it soon.
You can work around it for an individual export if you don't care about the Steam in-game overlay: open package.json and under the "settings" key, add "allow-host-input-processing": false. That puts it in the mode where gamepad input works but the Steam in-game overlay doesn't.