Here's why:
How penetration is calculated
In Menu Trends, penetration reflects the percentage of restaurants in a given universe that menu a particular item. When viewing Total U.S., a chain is counted once across the full dataset.
However, when viewing by region, chains that operate across multiple regions are counted separately in each region where they appear. This means a chain with locations in several regions will contribute to the penetration calculation for each of those regions individually — which can result in regional penetration figures that appear higher than the Total U.S. number.
The short version:
A chain that spans multiple regions gets counted once for Total U.S., but once per region it appears in — so regional pen can naturally run higher.