This is a good question.
It used to be that whatever day you checked in was the rate for your entire stay. I miss those days. Disney has now gone to a day by day rate. This has been lately including almost all discounts. However, sometimes not. It tends to be hit or miss. Even last June with the 4/3 discount, some people were getting the discount even if they checked in on the last day and others weren't. Usually with
free dining it doesn't tend to be a problem. Room only discounts it has been varying.
The biggest suggestion I can give you is to call and simply ask what the rates/cost would be. I've never had a problem with a CM giving those costs.