Yes, it is still possible with the component to use an inherited timer (so user can choose this). It is just that with the Kinetis SDK all the existing LDD/basic components are not working any more.
But if you select to use a non-SDK project, you have the most flexibility: LDD timer, non-LDD timer or RTOS Tick counter.
If your RTOS tick counter is fast enough (say 1 kHz), then I think the accuracy is good enough.
If you have a 100 ms period, well, then things are probably not that good any more
Erich