CLI applications benefit greatly from configurable options, and an effective method to provide this functionality is through the use of CLI flags, which are prefixed with a dash. These flags allow users to customize application behavior easily, such as toggling the display of specific outputs like word, line, or byte counts. In Go, implementing these flags involves utilizing the `flag` package, which supports the definition and parsing of various flag types, including boolean flags. The process includes defining the flags, providing default values, and setting usage messages that enhance user experience by clarifying usage through the help command. Additionally, structuring related flags into a cohesive type can simplify management and extensibility. This lesson underscores the significance of effectively incorporating CLI flags to enhance user interaction and application functionality while adhering to good coding practices such as encapsulation and testing.