Sorry for editing this post so much, but I changed my mind a minute after posting and no one had replied to it yet:

These are topologically different:

my $ar1=[$x,$x];
my $ar2=[$y,$z];
[download]

But these are the same:

my $ar3=[$x,$x];
my $ar4=[$y,$y];
[download]

That is, the comparison should care about the addresses of the references, but it should care about loops. Another way of looking at it is: deeply equivalent references should have the same canonical representation when dumped. Compare the following:

# $ar1
$VAR1 = [
          {},
          $VAR1->[0]
        ];

# $ar2
$VAR1 = [
          {},
          {}
        ];

# $ar3
$VAR1 = [
          {},
          $VAR1->[0]
        ];

# $ar4
$VAR1 = [
          {},
          $VAR1->[0]
        ];
[download]