I couldn't get your town to load because I don't have all those mods. The game seems to consider buildings set to "Off" as being empty. The game seems to apply the Full Indicator to only specific types of buildings. For example, only to Small Chapels, only to regular Chapels, or only to Parish Houses.
Make a bunch of different churches and play with turning them on/off and demolishing and see what happens.
The game didn't seem to care about <abbr title="Colonial Charter">CC</abbr> verse Non-<abbr title="Colonial Charter">CC</abbr>. The game seemed to care about precisely what type of building. It's just the indicator that messed up. The functionality worked fine on my end.
For example, I made 5 Small Parish Houses (that hold 80 each so 400 total) in my town of 500+ People. When all the Parish Houses were on I got the full indicator. When I turned one off there was no full indicator on the Parish Houses. If I had a singular chapel of another type and that other chapel was full then only that chapel would have the full indicator.
