I saw the prompt Called by the default initialization function, but I did not find where Board_InitBootPins was called.
The RTD example calls:
Siul2_Port_Ip_Init(NUM_OF_CONFIGURED_PINS_PortContainer_0_BOARD_InitPeripherals, g_pin_mux_InitConfigArr_PortContainer_0_BOARD_InitPeripherals);
Have you considered calling the remaining Function groups by their names?
Siul2_Port_Ip_Init(NUM_OF_CONFIGURED_PINS_PortContainer_0_BOARD_InitPeripherals, g_pin_mux_InitConfigArr_PortContainer_0_BOARD_InitPeripherals);
Siul2_Port_Ip_Init(NUM_OF_CONFIGURED_PINS_PortContainer_1_BOARD_InitPeripherals, g_pin_mux_InitConfigArr_PortContainer_1_BOARD_InitPeripherals);
