The Fonts & Colors preferences pane has to do with AppleScript formatting, that is, the pretty-printing of compiled scripts. This facility is provided by AppleScript (as part of the decompilation process), not by Script Debugger. This preference pane thus accesses AppleScript’s preferences.

You can select multiple lines of the table and change their font or color all at once.

Changes are not sent to AppleScript until you click the Apply button. When you do, any compiled scripts that are open now, as well as any compiled script files that you open or create in the future, will take on the formatting you have specified. To cancel (changing your mind without applying your changes), switch to another pane, or close the window.