It's working as intended =) You're getting the right ideas now.
As i said, CubeMX does not know anything about touch controllers. This is BSP! It only does MCU configuration.
The application template comes with a working project. What we did is start from cubemx/generator (like you) and then manually made the touch controller work, manually configured SDRAM and QSPI, because that's how you would bring up a custom board. The touch controller is display/board specific! CubeMX has no clue, so you need to write the code yourself. And that's what we did for you, in all the application templates.
/Martin