Hello Jan:
Sorry for the confusion created so far. There is no error or problem with the header files, you are just looking at two different kind of headers and the fact that the name is the same is just an inconvenience.
Please read my last response in the next thread: KL25Z CMSIS-Core/CMSIS Peripheral Access Layer headers
And the next discussion as well: why bare-metal head file is so different from PE head file even with same version like MK21F12.h
You can read the abstract for each type of MK20D5.h:

In KDS you may find both kind of files in these paths:
- C:\Freescale\KDS_3.0.0\eclipse\ProcessorExpert\Config\PE\CPE\wizard_data\wizards\kds\MK20D5\Include
- C:\Freescale\KDS_3.0.0\eclipse\ProcessorExpert\lib\Kinetis\iofiles
The No CMSIS compliant header is now only used when creating a project with Processor Expert using legacy LDD components (No KSDK).
There are macros not present in the CMSIS file, but you can easily replace such register accesses. In your case this would be the code:
PORTA->PCR[18]
PTC->PSOR
I hope this helps to clarify.
Regards!
Jorge Gonzalez
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