The following will demonstrate an approach to define a &SUPEREND::DESTROY which is run after all other global DESTROY()s happend.

use strict;
use warnings;

package Blubb;

sub new {
   my $this = bless {a=>42};
   $this->{circular} = $this;
}

sub DESTROY {
    warn "DESTROY ". __PACKAGE__;
}

package SUPEREND;

no warnings 'redefine';

my $orig_destroy= \&Blubb::DESTROY;
my $persist = bless { count=>0};


*Blubb::DESTROY= sub {
   $orig_destroy->(@_);
   warn "Mini END";
   $persist->{count}++;
};




sub DESTROY {
    warn "DESTROY after $_[0]->{count} destroys ". __PACKAGE__;
}



package MAIN;

my $b = Blubb->new;
my $c = Blubb->new;
my $d = Blubb->new;
[download]

DESTROY Blubb at c:/tmp/pm/destruct_end.pl line 12 during global destr
+uction.
Mini END at c:/tmp/pm/destruct_end.pl line 25 during global destructio
+n.
DESTROY Blubb at c:/tmp/pm/destruct_end.pl line 12 during global destr
+uction.
Mini END at c:/tmp/pm/destruct_end.pl line 25 during global destructio
+n.
DESTROY Blubb at c:/tmp/pm/destruct_end.pl line 12 during global destr
+uction.
Mini END at c:/tmp/pm/destruct_end.pl line 25 during global destructio
+n.
DESTROY after 3 destroys SUPEREND at c:/tmp/pm/destruct_end.pl line 33
+ during global destruction.
[download]

Please note, that this can be extended to be a generic solution, because SUPEREND could parse all packages available and monkeypatch all DESTROYs there (if existent)

Since $persist is referenced it's DESTROY will be run last.

For syntactic sugar one could also make SUPEREND export a function SUPEREND(&) accepting a codeblock which is run by the DESTROY of $persist.