mcc compiles matlab files into executable and Application Compiler app does the same thing along with packaging the files. Application compiler also creates a web installer additionally.
You perform the same functions using either the compiler apps or the mcc command-line interface.
You can always refer the corresponding mcc command in 'PackagingLog.html' when you are compiling through Application Compiler.
The interactive menus and dialogs used in the compiler apps build mcc commands that are customized to your specification. As such, your MATLAB® code is processed the same way as if you were compiling it using mcc.
Compiler app advantages include: You perform related deployment tasks with a single intuitive interface. You maintain related information in a convenient project file. Your project state persists between sessions. You load previously stored compiler projects from a prepopulated menu. Package applications for distribution.