Matlab Coder does not support GUI code as far as I am aware. It wouldn't really make sense since the GUI is Matlab-based and C++ code would require additional libraries and whatnot to reproduce a UI anywhere close to Matlab.
I don't really understand what you are trying to do. Matlab Compiler creates a standalone deployable executable, Matlab Coder converts supported code to C++ (and some other languages I forget probably) code for use either externally or via mex within your Matlab application.
The standalone GUI created by Compiler will always need the Matlab Compiler runtime though. If you don't want that then you'll have to write a GUI in some other language to support code ported by Matlab Coder.
