In my opinion, it very depends on what "matrix" functionalities do you need to implement. For instance, for some jobs, I do not see anything wrong in the simplest HoH representation - nested hash, as you noticed above, plus methods (not error/warning proof):

my %matrix = ('R-Linux'  => {confdir=>'abc'},
              'R-Solaris'=> {scriptpath=>'def'});
sub item {
  my ($os,$what,$value) = @_;
  $matrix{$os}{$what} = $value if 3==@_;
  return $matrix{$os}{$what};
}

sub delete_item {
  my ($os,$what) = @_;
  delete $matrix{$os}{$what};
}

...
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