Keep it simple: use set_att instead of id_seed and format the id value as you want:

#!/usr/bin/perl

use strict;
use XML::Twig;

my $string = '<xml>
<p>here the paragraph comes</p>
<p>here the paragraph comes</p>
<p>here the paragraph comes</p>
<p>here the paragraph comes</p>
<a>here the paragraph comes</a>
<a>here the paragraph comes</a>
<a>here the paragraph comes</a>
<a>here the paragraph comes</a>
<a>here the paragraph comes</a>
<a>here the paragraph comes</a>
<a>here the paragraph comes</a>
<a>here the paragraph comes</a>
<a>here the paragraph comes</a>
<a>here the paragraph comes</a>
<a>here the paragraph comes</a>
<a>here the paragraph comes</a>
</xml>';

my $i;
my $j;
my $twig = new XML::Twig(
                    
    twig_handlers => {
        p => sub { $_->set_att(id => sprintf "fig%02d", ++$i) }, #gene
+rate id
        a => sub { $_->set_att(id => sprintf "sec%02d", ++$j) }, #gene
+rate id
                    
                                         },
    pretty_print => 'indented' #print format
);


$twig->parse($string);
$string = $twig->sprint;

print $string;
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