The solution for that problem (nothing to do with PDF::API2, btw) would be to patch my patch :)  i.e. pass $row_cnt instead of $rows_counter to the callback function (from within PDF::Table). The latter counts all displayed rows irrespective of whether they're headers, while the former counts data rows only.

And while you're at it, you might also want to pass $first_row, which indicates whether it's a header row — so you can then write

        cell_render_hook => sub {
            
            my ($page,  $row, $col, $is_first_row,  $x, $y, $w, $h) = 
+@_;

            if (( $col == 0) && (!$is_first_row) ) {

            # ...instead of this (which doesn't work)
            # if (( $col == 0) && ($row >= 1) ) {
                                 
                my $t = $row-1;
                ...
[download]

For reference, the corresponding modified patch to PDF::Table would then look like this:

    if (ref $arg{cell_render_hook} eq 'CODE') {    
        $arg{cell_render_hook}->(
                                 $page,
                                 $row_cnt,
                                 $j,
                                 $first_row,
                                 $cur_x,
                                 $cur_y-$row_h,
                                 $calc_column_widths->[$j],
                                 $row_h
                                );    
    }
[download]