YES. Our process is over. Received the COPR and the passport back! Hey, thanks to everybody who submitted their experiences... although reading everybody else's application makes me feel incompetent, unorganised, and have not done my homework prior to handing in our own application!
oh, one more note, i thought the reason for submitting the passport was so that a sticker or a stamp will be physically attached it. But I was wrong and I have no idea why they actually need the passport, perhaps to check if it was the real thing maybe? My wife's passport is from Hong Kong SAR, and as such, is visa-free for entry. So, in actual case, they just need to send us the COPR and she could enter using such.