Yes, really. No harm in trying your luck, but it is not part of your rate and not part of F&B spend or such other points earning spend activities. Hence, that extra $ spend on upgrades or Club access or both should not earn points. (If you do, you got lucky). You'll earn based on your original booked, paid rate of course and if the rate is qualifying it will accrue qualifying nights as well.

I had this many times at IC Bali, IC BKK, IC HCM (Saigon), IC KUL, IC GS HKG, IC ANA Tokyo, etc. where at times we would pay for Club upgrade at check in or negotiated upfront and that amount spend on the upgrade component never earned points. It all comes down how the staff "codes" that spend in the Opera (or new Amadeus, depending on property) Reservation/PMS (property management system). YMMV.