Same issue. I had to comment this line:
CONFIG_CHIP_NFC_COMMISSIONING=y
I also had to tinker with quite a few files to get the paths recognized.
It also seems the nfc_t2t_lib.h file included in
#include <nfc_t2t_lib.h>
Error:
NFCOnboardingPayloadManagerImpl.cpp is missing in the SDK
obj/src/platform/nrfconnect/nrfconnect.NFCOnboardingPayloadManagerImpl.cpp.o
c:\ncs\v3.1.0\modules\lib\matter\src\platform\nrfconnect\nfconboardingpayloadmanagerimpl.cpp:28:10: fatal error: nfc_t2t_lib.h: No such file or directory
28 | #include <nfc_t2t_lib.h>
| ^~~~~~~~~~~~~~~
compilation terminated.
It looks a lot like DIY.