Hi Claudio,
sorry for delay, NXP community was under maintenance and then in read-only mode.
If you use MCUXpresso IDE 11.2, then the FRDM-KE16Z should support Pins,Clock and Peripherals tools. If you have already create MEX configuration, you can switch between Config Tools using main menu "ConfigTools"

If you haven't created the MEX (Config Tools) configuration yet, you can create it using either "Quickstart Panel" view:

Or right click on workspace SDK based project folder:

The mentioned downloaded ZIP file is used for situations when the MCUXpresso IDE/Config Tools for any reason does not have connection to the internet and the Config Tools data cannot be downloaded automatically on-the-fly. These data can be downloaded on mcuxpresso.nxp.com and imported using "File | Import..." and using wizard "MCUXpresso Config Tools => Import processor data".

Regards,
Libor