if(exists($coordinates->{$group})) {
  if(exists($coordinates->{$group}->{$id})) {
    if(exists($coordinates->{$group}->{$id}->{$stage})) {
      ...
    }
  }
}

##</code><code>##

my $result = do_stuff_in_hash_without_autovivifying(
  sub {
    my $hash_to_work_on = shift;
    # do stuff here
  },
  $coordinates,                 # initial hash
  $group, $id, $stage, 'coords' # list of keys to traverse
);

sub do_stuff_in_hash_without_autovivifying {
  my($sub, $hash, @keys) = @_;
  if(@keys && exists($hash->{$keys[0]}) {
    return do_stuff_in_hash_without_autovivifying(
      $sub,
      $hash->{$keys[0]},
      @keys[1 .. $#keys]
    );
  } else {
    return $sub->($hash);
  }
}

##</code><code>##

use Tie::Hash::Vivify;
use Data::Dumper;

my $hash = Tie::Hash::Vivify->new(sub {
  die("No auto-vivifying! Bad programmer! No bikkit!\n".Dumper(\@_))
});