It's not a given that room changes disqualify you from earning the rebate, but in the past it was possible that the hotel changing the booking removed CWT's commission from the reservation, meaning they didn't get paid, and since the T&Cs say that all changes have to be made through Citi, they used that as an excuse to not pay you.

That said, extra charges are fine. The reimbursement process is not automatic, so if they see a charge for more than what they were expecting you to pay, you should be fine. (I believe they usually get a copy of your folio to check against.)

If you get a comp upgrade at the hotel, you'll almost certainly be OK. Paying for an upgraded room is where you might get into trouble.