The inability to compile Simulink's generated code within the Arduino IDE is expected. The Arduino IDE uses its own language (the files are INO-files) which are then converted to C-code. This can often go unnoticed as Arduino's language is so similar to C (it is actually a subset of C).
The Simulink Support Package is generating C-code directly (bypassing the INO-file). However, there is a way to modify the generated C-code before deploying an application to the target.
1) Select the option to "Generate code only" in the Simulink Code Generation Configuaration Parameters and generate code for the Arduino embedded target.
2) Open and modify that generated C-code using any C-code IDE.
3) Use the MK-file generated by Simulink to compile and build the application for the Arduino.
4) Use the 'avrdude' tool to deploy the application to the Arduino.
The following website provides a good explanation of the Arduino IDE programming/compilation process (and how to bypass using the INO-file).