Hello,
For your purpose, the best option is, as you said, STOP2 because the bus clock remains active, but FTM (FlexTimer module) is OFF in the STOP modes.
The LPIT has full functionality in the STOP2, so, you can use it. However, the timers have some disadvantages.
The LPIT you can read only in the interrupt. The LPTM is only 16-bit and RTC is accurate when you have an external clock.
So, it depends on your application.
Also, I would like to recommend you to look at Table 38-4. Module operation in available power modes to see each module functionality in this mode.
Also, you can look at AN5425. There the STOP mode entry sequence can be seen.
https://www.nxp.com/docs/en/application-note/AN5425.pdf
AN5425SW
https://www.nxp.com/webapp/Download?colCode=AN5425SW&docLang=en
I hope it helps.
Best regards,
Diana