Hello Jmir,
Both timers may generate the required signal, albeit they have different features depending on your application:
The FTM (Flex Timer Module) is very flexible, as the name suggest, as it has additional modes like input capture or output compare, for example.
The LPIT (Low-power Periodic Interrupt Timer) can operate in low power modes so it’s mostly used for operations required in low power mode.
In regards as a tick timer for a real time control system, as Mark mentioned, in Kinetis microcontrollers usually use the SysTick timer is used instead, which is part of the Cortex-M0+ features.
Regards,
Gustavo