The point of XML::Simple
is to have a way to specify a Perl data structure with XML, and to serialize that data structure into some valid XML representation. It's not meant for very specific structure control in either direction, and if you find yourself trying to tweak things to get it to be precisely as you wish, you've probably gone beyond its abilities.
If you want to manage precise XML transformations, look in to XML::LibXML or the higher-level xsh scripting language. I did a column on that a while back.