Is there a way to use the KDS like a traditional IDE for embedded MCU? I means setting up the pheripheral by .h and .c files, for e.g. MKL25Z4.h. Without moving the Product Expert Route.
Yes, it is essentially Eclipse.
Any plugin tools are "on top" of its basic functionality (editing, managing a build, connecting to targets, downloading and debugging) and are therefore options.
I use KDS with the uTasker project: http://www.utasker.com/kinetis.html which contains all processor support without need for any automation.