From what I’ve read of architecture, a variety of ceiling heights tends to help. To make a room with high ceilings more cozy, there are often alcoves with lower ceilings, for things like beds and tables. Sometimes drop ceilings will be added for part of the space to create a separation.

People in a large open restaurant with high ceilings will tend to avoid sitting in the middle.

Using churches for examples of how residential space should look isn’t very convincing. Most people wouldn’t want to live in a church.