To begin with, note that there is a difference between the Limit Configuration that one does from the toolbox, and actually using the limit in a measure or in a chart.
Flow allows you to set up one or more "simple" limit definitions. These limits can be used for various functions (i.e. targets not achieved, data validation checking, bonus target achieved, etc.). Once these Limits have been configured, they can be used to configure Measures’ limits or targets. A Measure can be configured with more than one Limit if required.
The settings in the top panel (named after the limit you've selected, in this case "Site) are used to configure the limit colors that are used in graphical charts.
The "Text" settings are used to configure the font colors that are used in text-based reports.