I left the plane on both HKG-TPE//TPE-NGO and HKG-BKK//BKK-SIN.

The NGO trip was in Y (got upgraded to J) + J, the SIN trip was J + Y (with miles upgrade to J, so it's still Y).

Yes, they'll give you two separate boarding passes. I'm not sure what happens if they don't scan the second one. Presumably you can tell the ISM that you've got two tickets. Actually on my two flights, the ISM knew I had separate boarding passes.

For the NGO flight, when I landed in TPE, they had a sign with my name on it. They checked I had my second boarding pass and did not give me a "transit card" as I wasn't a transit passenger.

Hope this helps.