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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