I set allowOpenFromManagedToUnmanaged and allowOpenFromUnmanagedToManaged to false, but this did not work, as unmanaged applications can still invoke the URL schemes of managed applications.

Sorry, there is a mistake in the above description. We do not use the Install Enterprise app command. Instead, we use the Install an App command with the ManifestURL supplied in the command

I applied the Managed Open In restrictions and they are not working. Bundle ID cannot be passed via custom URL scheme as it is invoked from a Webpage. Since the Webpage is not aware of the application it is running in, it cannot send the source bundle identifier while invoking the custom URL scheme.

I've filed a Feedback Assistant as suggested. The Feedback ID is 16107305. Please look into it.

@Device Management Engineer, can you please provide an update on this

Still waiting for a reply on this or the feedback assistant. Please help out here