That doesn't make sense to me either. I'd understand if he meant that the upgraded room might no longer be available. But it seems to me that if an upgraded room is available, and they were originally planning to comp you that upgraded room, then they should still be willing to do that.
I'm staying at the WL, too, and faced the same options. Group reservations called to say that they saw we had reserved a standard room for the week. And that as a "surprise", my wedding planner had reserved a honeymoon suite for us for our wedding night, as our comped room. The reservation agent said she was calling to make sure we wanted that, since it would mean moving from room to room. I said that was fine. And then later on, I realized that moving on our wedding day really would be inconvenient. Plus, since I'll be getting my hair/make-up done in my room (at 5am) and a bunch of my girlfriends have said they want to be there while I'm getting ready, I decided it'd be better to already be in a suite-sized room the night before my wedding. So... I decided we'd get a standard room for the first two nights. Then I'll move to the suite the night before the wedding. DF will bunk with someone else. Then we'll both be in the suite on the wedding night. And then move back to a standard room the next day, for the rest of the trip.