In this case, you should just have to exclude the Middlewares/ST/STemWin/Simulation folder from the build; it is delivered by Segger to allow compiling your GUI in Simulation mode on your Windows box but, obviously, should not be compiled for the target.
To do that you right click on the folder then Properties go to the C/C++ Build tab and select Exclude resource from build. Note furthermore that emWin can work either with or without FreeRTOS, so you must compile only one of the Middlewares/ST/STemWin/OS/GUI_X_OS.c (with RTOS) or GUI_X.c (without RTOS) using the same mechanism. You must also in Middlewares/ST/STemWin/Config, update GUIConf.h if needed (at least regarding the use of RTOS or not) and exclude all .c files (the templates and C files are just examples to use as a base when supporting your own board).
I just check it (with FreeRTOS) and it compiles. I can’t test it as I don’t have this board here but it should work, although not displaying anything as you have to at least provide something to display.
To go further I can only urge you to look at the STemWin sample project in the HAL firmware (just check the Extract all firmware in separate folder in the firmware selection tab when creating the project (this will take some time...) and look in the created (closed) STM32Cube_FW_F7_V1.7.0 project in Projects; However there is no simple demo application (in Applications) for the discovery board, for STemWin, just the full-fledged Demonstration that you can open by File >> Import... >> General >> Existing project into workspace, then select the proper sub-directory of the firmware project (Projects\STM32F769I-Discovery\Demonstration\SW4STM32\STM32F769I-Discovery_Demo in this case) and click OK. You then have a program that uses almost all possibilities of the board.
Another alternative when wanting to use additional firmwares is to have CubeMX generate the project and initialize things; it was developed just for that. Mbed may be an alternative also but it is currently not integrated so well with System Workbench for STM32 (we were not involved in this integration)
Anyway you can’t choose any selection of firmwares for a given evaluation board and then expect to get a working program just with the push of a button. There is quite a lot of documentation (for STemWin there is a detailed user manual in the provided folder) that you may have to read and understand before being able to create your own project “from scratch”.