After some tinkering with Kbuild system I ended up with conclusion that a most straightforward way to handle situation like this, is to filter-out warning messages from make
output in the outer makefile:
$(MAKE) -C $(KDIR) M=$$PWD 2>&1 \
| grep -v '^WARNING:.*exported twice\. Previous export was in'
or w/o sacrificing STDERR and squashing it into STDOUT, but it requires bash
:
bash -c "$(MAKE) -C $(KDIR) M=$$PWD 2> >( grep -v '^WARNING:.*exported twice\. Previous export was in' )"