Here are the Fannie Mae requirements for differences in living area that effect the majority of all residential loan types.
Only finished above-grade areas can be used in calculating and reporting of above-grade room count and square footage for the gross living area. Fannie Mae considers a level to be below-grade if any portion of it is below-grade, regardless of the quality of its finish or the window area of any room. Therefore, a walk-out basement with finished rooms would not be included in the above-grade room count. Rooms that are not included in the above-grade room count may add substantially to the value of a property, particularly when the quality of the finish is high. For that reason, the appraiser should report the basement or other partially below-grade areas separately and make appropriate adjustments for them on the Basement & Finished Rooms Below-Grade line in the Sales Comparison Approach adjustment grid.
The appraiser did follow the correct guidelines if you have a split-level home. Since the basement area is being accounted for as basement living area, there would be no impact to value assuming your home is being compared to other homes with basement living area. If you look at the sales comparison grid were your home is being compared to the other comparables you will see this.
If your home is 1,500 Sq Ft above grade and 1,500 Sq Ft of basement area the market would still recognize your home as 3,000 Sq Ft regardless of how the Sq Ft its broken out in the appraisal.