You misunderstood me.
Native (i.e. boards/native and cpu/native) does not touch the includes for RIOT and the application. But it needs the host system definitions, so it can't use the RIOT includes to translate its own sources. That is why native is translated like `$(CC) $(CFLAGS) NATIVEINCLUDES)` where `$(NATIVEINCLUDES)` are only the RIOT headers which are needed for native. If you merge `$(INCLUDES) into `$(CFLAGS)` this does not work anymore.