Probably that is caused by the perl_build buildsystem not being detected
for a package that has a Makefile.PL, and so MODULEBUILDRC is not
overridden. So, I could add it there too, but then it's also possible for
it to be run from a Makefile.. so I could add it to dh_auto_*. But
then there are packages that don't use those. So I conclude that dealing
with this in debhelper is out of its scope, and this needs to be fixed
at a higher level, probably dpkg-dev.