A neat way to do it would be to use roles. Say, for example, you want to monkey-patch "Example::Module". Then you'd publish your patch like this:

# lib/Example/Module/Enhanced.pm
use 5.008009;
use strict;
use warnings;

package Example::Module::Enhanced;

use constant PATCH  => __PACKAGE__ . '::Trait';
use constant TARGET => 'Example::Module';

sub import {
  my ( $me, $arg ) = @_;
  'Role::Tiny'->apply_roles_to_package( $me->TARGET, $me->PATCH )
    if defined($arg) && $arg eq '-auto';
}

sub patch_object {
  my ( $me, $obj ) = @_;
  'Role::Tiny'->apply_roles_to_object( $obj, $me->PATCH );
  return $obj;
}

# Yes, it's safe to define this second package in the same file...
package Example::Module::Enhanced::Trait;

use Role::Tiny;

sub some_new_method {
  my ( $self, @args ) = @_;
  ...
}

around some_existing_method => sub {
  my ( $orig, $self, @args ) = @_;
  ...;
  my $result = $self->$orig( @args );   # call original method from Ex
+ample::Module
  ...;
  return $result;
};

1;
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With a patch like that, people have two ways of using it. They can use it selectively:

use Example::Module;
use Example::Module::Enhanced;

my $obj  = Example::Module->new;
my $obj2 = Example::Module->new;

Example::Module::Enhanced->patch_object( $obj );

# Now $obj1 has your monkey patch, but $obj2 is still non-patched!!!
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Or they can use it everywhere:

use Example::Module;
use Example::Module::Enhanced -auto;

my $obj  = Example::Module->new;
my $obj2 = Example::Module->new;

# All Example::Module objects are monkey-patched!
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Note that you're not uploading any modules or packages named Example::Module. So there shouldn't be any versioning/permissions issues with your upload.

Above code is untested, but should work.