$hnr{'MAIN'}        = { %list1 };
$hnr{'MAIN'}{'ZOP'} = { %list2 };
$hnr{'MAIN'}{'AP'}  = { %list2 };
[download]

$hnr{'MAIN'}        = \%list1;
$hnr{'MAIN'}{'ZOP'} = \%list2;
$hnr{'MAIN'}{'AP'}  = \%list3;
[download]

{ %tied } creates a new (unordered) hash with a copy of %tied contents. That's not what you want,

Update: Alternatively, I think tying anon hashes is perfectly fine:

use Data::Dumper qw( Dumper );
use Tie::IxHash  ();

tie my %hnr, 'Tie::IxHash';

%hnr = (
   ZOP  => {},
   AP   => {},
   Exit => undef
);

tie %{$hnr{'MAIN'}{'ZOP'}}, 'Tie::IxHash';
tie %{$hnr{'MAIN'}{'AP'} }, 'Tie::IxHash';

my @zop_and_ap_init = (
   Dev  => undef,
   Con  => undef,
   Test => undef,
   Exit => undef,
   New  => undef,
);

%{$hnr{'MAIN'}{'ZOP'}} = @zop_and_ap_init;
%{$hnr{'MAIN'}{'AP'} } = @zop_and_ap_init;

print Dumper(\%hnr);
[download]