I finally came up with a solution. you can choose which field to diff, and then print a diff report based on that field

use strict;
use warnings;
if ($#ARGV < 1) { die "usage csvout_compare.pl <csvoutout1> <csvout2> 
+<csvoutout3>.....\n"};
my $f=0;

my %allhash;
my @indexes_to_print;
my %data;
my @line;
my $index;
foreach my $files (@ARGV) {
    $f++;
    open FILE,$files or die "Cannot open $files\n";
    print "Opened $files \n";
    while (<FILE>) {
        next if (/csvout_ID/);
        chomp;
        @line = split(/,/,$_);
        $index = $line[0].".".$line[1];
        $allhash{$index} = 1;

        $data{$f}{$index} = "$_";
            }
    close FILE;
}

foreach $index (keys %allhash) {
    my @temparray;
    my $flag = 0;
    #First lets take all those indexes which are not in all files
    foreach my $dataset (keys %data) {
        if (!(exists $data{$dataset}{$index})) {
            push (@indexes_to_print,$index);
            #delete $allhash{$index};
            $flag = 1;
        }
    }
    next if ($flag eq 1);

    #Now we take those indexes where the Final result is different
    for (my $i=1;$i<=$f;$i++) {
        my @temp = split(/,/,$data{$i}{$index});
        $temparray[$i] = $temp[2];
        if ($i>1) {
            if ($temparray[$i] !~ $temparray[$i-1]) {
                push (@indexes_to_print,$index);
            }
        }
    }
}
#uniquify @indexes_to_print
#
 my %seen   = map { $_, 1 } @indexes_to_print;
 my @unique_indexes = keys %seen;

 foreach my $index (@unique_indexes) {
     print "$index";
    for (my $i=1;$i<=$f;$i++) {
        if (exists $data{$i}{$index}) {
            my @temp = split(/,/,$data{$i}{$index});
            #print ",$i,$temp[2]";
            print ",$i";
            foreach (my $j=2;$j<=10;$j++) {
                if (exists ($temp[$j])) {
                    print ",$temp[$j]";
                } else {
                    print ",";
                }
            }
        } else {
            print ",$i,NA,,,,,,,,";
        }
    }
    print "\n";
}
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