Yes, you may change whatever you wish. For the specific case of the backlight (TIM4), there is dedicated function (LCD_SetBackLight) in CircleOS.
HOWEVER:
The only important rule consists in restoring the initial state when exiting from any application (we have to keep in mind the multi-application concept of the CircleOS). Indeed, if you don't restore properly the context of the peripherals, you should ceate some problems for the next applications that will be launched.
By default, the function MENU_Quit() restores the main settings of the Primer, but it does not reset all the internal peripherals. This task is attached to each application and must be done when exiting the application.