Could it be that you're suppose to use twig_handlers instead of twig_roots, since you don't want body to become a root node? The example from the module's documentation is: (irrelevant details omitted)
my $twig=XML::Twig->new(
twig_handlers => {
title => sub { $_->set_gi('h2') }, # Change title tags to h2.
para => sub { $_->set_gi('p') }, # Change para to p.
hidden => sub { $_->delete; }, # Remove hidden elements.
list => \&my_list_process, # Process list elements.
},
pretty_print => 'indented', # Output will be nicely formatted.
);
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