Hello Marco Coelho,
Yes, it really missing the PIT module , I will report it to MCUXpresso config tool development team.
Which chip do you used ? Does it have FTM module ?
If yes, you config it to periodic interrupt. Also in SDK package , there is FTM demo as a simple timer :
SDK_2.3.0_FRDM-K64F\boards\frdmk64f\driver_examples\ftm\timer
Hope it helps
Alice