Hi,
typically, within a customer project the makefile (or the project settings) are modified and adapted to the dedicated needs, e.g. to add additional BSP drivers or own DeviceDriver modules.
Within our Build Environments we follow a template approach containing one universal makefile that is suitable to all examples, all color formats, with or without FreeRTOS,....
In case of STM32, Embedded Wizard Studio generates C code (*.c/*.h) and a file ewfiles.inc, that can be used within a makefile. But the makefile itself (or the project file) is not related to the GUI development.
Best regards,
Manfred.