In light of the SA Chain Game using a save that has city barriers removed, I've added a few options and more info the SA download page.
The Enabled IPLs link in the Save Information section will display the status of a few select IPLs, notably the ones used for the city barriers and three others that are set by the IPL Flags modification if v1 or v2 is selected.
The IPL Flags modification now has two new options, v1 Disabled Barriers and v2 Disabled Barriers. These will remove the city barriers regardless of mission completion. The original v1 and v2 options are now called v1 Story Barriers and v2 Story Barriers.