No, it's just a new hat, but on the other hand, there is nothing wrong on using globals for storing global data and for most apps, configuration data is just global data.

Anyway, I would break the configuration module in two:
a) a generic class abstracting the configuration access logic.
b) a module implementing a singleton to access the global configuration specific to the app.

For example:

class Config::Foo;

package Config::Foo;

sub new {
  my $class = shift;
  my $fn = shift;
  ## read the configuration file here
  ## ...
  bless $this, $class 
}

sub get {
  my $this=shift;
  my $key=shift;
  my $default=shift;
  exists $this->{$key} ? $this->{$key} : $default;
}

sub set {
  my $this=shift;
  my $key=shift;
  my $value=shift;
  $this->{$key}=$value;
}

1;

---

package MyApp::Config;

use Config::Foo;
require Exporter;
our @EXPORT=qw(config);
our @ISA=qw(Exporter);   ## (updated!)

my $config;

sub config {
  $config=Config::Foo->new('/etc/myapp.conf')
    unless defined $config;
  $config;
}

1;

---
# and in your app

use MyApp::Config;

my $foo=config->get(foo);
config->set(bar => 'new_bar');
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