my %file1_hosts = (
   bobssite => {
      'bobssite.autossl.net' => 1,
      'www.bobssite.com'     => 1,
      'bobssite.dealer.net'  => 1,
   },
   billssite => {
      'billssite.autossl.net'  => 1,
      'www.billssite.com'      => 1,
      'www.billsothersite.com' => 1,
      'bobssite.dealer.net'    => 1,
   },
);

##</code><code>##

sub compare_aliases {
   my ($host, $file1_aliases, $file2_aliases) = @_
   my %aliases = map { $_ => 1 }
      keys(%$file1_aliases),
      keys(%$file2_aliases);
   for my $alias (keys(%aliases)) {
      if (!$file1_aliases->{$alias}) {
         ...
      }
      elsif (!$file2_aliases->{$alias}) {
         ...
      }
   }
}

sub compare_hosts {
   my ($file1_hosts, $file2_hosts) = @_
   my %hosts = map { $_ => 1 }
      keys(%$file1_hosts),
      keys(%$file2_hosts);
   for my $host (keys(%hosts)) {
      if (!$file1_hosts->{$host}) {
         ...
      }
      elsif (!$file2_hosts->{$host}) {
         ...
      }
      else {
         compare_aliases($host,
            $file1_hosts->{$host},
            $file2_hosts->{$host},
         );
      }
   }
}

compare_hosts(\%file1_hosts, \%file2_hosts);