This is a cool idea! I'm not sure if my tactic is much better but I thought of using a source filter:

package CFGPL;

use warnings;
use strict;

our $Comment_Start = '#';

sub import
{
    shift;
    $Comment_Start = quotemeta shift if @_;

    # Read in only our commented code...
    open my $own_src_file, '<', $0;
    my @perl_code = grep { /^$Comment_Start/ } <$own_src_file>;
    close $own_src_file;

    die "Config file has no code in comments\n" unless @perl_code;

    # Write it back to config file and erase uncommented stuff!
    open STDOUT, '>', $0;
    print @perl_code;
}

# Filter out the leading comment and runs the code...
require Filter::Simple;
Filter::Simple::FILTER( sub { s/^$Comment_Start//gm; } );

1;
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Easy to invoke like: perl -MCFGPL config.file.