Another approach is to subclass the module, or intercept calls. For a work project, I wasn't happy with the Pod::Html output, so I hacked in some changes that vary depending on the version:

sub per_version {
  if ($Pod::Html::VERSION eq '1.01') {
    # perl5.005_03
    *Pod::Html::process_text2 = \&Pod::Html::process_text1;
    undef *Pod::Html::process_text1;
    *Pod::Html::process_text1 = \&my_process;
    @options = qw/ --recurse --header /;
  } elsif ($Pod::Html::VERSION =~ /^1\.0[34]$/) {
    # perl-5.6.0, 5.6.1, 5.8.0
    *Pod::Html::process_L2 = \&Pod::Html::process_L;
    undef *Pod::Html::process_L;
    *Pod::Html::process_L = \&my_oldprocess;
    @options = qw/ --recurse /;
  } else {
    die "Don't know how to hack Pod::Html v$Pod::Html::VERSION\n";
}

sub my_process ($$;$$) {
  my($lev, $rstr, $func, $closing) = @_;
  my $closer = '>' x (($closing||0) + 1);
  if ($func && $func eq 'L') { 
    # suppress 'the ... manpage' markup
    $$rstr =~ s{^ 
      ^ ( \w+ (?: ::\w+ )* )
      (?: -(?!$closer)> (\w+) )?
      (.*?) (\s* $closer)
    }{
      defined($2) ? qq{$1-E<gt>$2$3|$1/"item_$2$4} : "$1$3|$1$4"
    }xe;
  }
  Pod::Html::process_text2($lev, $rstr, $func, $closing);
}

sub my_oldprocess {
  my($str) = @_;
  $str =~ s,^(\w+(::\w+)*)$,$1|$1/,;
  Pod::Html::process_L2($str);
}
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This approach isn't always the right one, but it's a useful tool to have.