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OP here. More information on the issue:
The app I'm building is an electron app.
I'm signing the app content using the command line tools. And then I'm packaging it as .pkg.
Transporter is apple's recommended app to upload app packages to MacOS App Store. It is supposed to find issues with package early on before submitting it to macOS App Store. All checks were passed.
I don't see how Xcode can be used(the app is written in javascript using electron, not in swift or objective C)
I have tried different permutation combination of signing with Apple ID, using provision profile, changing .plist file, etc.