The "kitchen sink" module for manipulating XML is XML::Twig. Consider:

use strict;
use warnings;
use XML::Twig;

my $xml = <<XML;
<outermost>
    <innermost>
        <first>1</first>
        <second/>
        <third>These spaces are to be preserved.</third>
    </innermost>
</outermost>
XML

my $twig = XML::Twig->new();

$twig->parse ($xml);
$twig->print();
[download]

Prints:

<outermost><innermost><first>1</first><second/><third>These spaces are
+ to be preserved.</third></innermost></outermost>
[download]