If you’re starting your journey with CX at NRT, you can ask them to print your HKG-TPE boarding pass. This should in theory flag you as a connecting passenger in their systems. If you do OLCI and print your own boarding pass you’re probably on your own.

From my personal experience, CX has been quite generous with offering protection when misconnecting on separate tickets. At least, on CX-CX connections. Still, there’s no guarantee of this.