Scientific and Engineering Contexts:
Percentage difference is very common in science and engineering to quantify the agreement between two different measurements or between a measured value and a theoretical value. It provides a standardized way to express error or discrepancy when there isn't a clear 'correct' starting point.
Business and Finance:
In business, you might use percentage difference to compare the sales figures of two different branches of a company in the same period, or to compare the cost of two different suppliers for the same material. It helps in making a relative comparison without implying one is the 'original' and one is the 'new'.