If there are only two "interesting" columns, ignore the rest. Consider:

use strict;
use warnings;

my $data = <<DATA;
CLS_S3_Contig100_st,CLS_S3_Contig100,53,10,0.3717
CLS_S3_Contig100_at,CLS_S3_Contig100,55,11,0.4321
CLS_S3_Contig100_st,CLS_S3_Contig100,57,10,0.3223
CLS_S3_Contig100_at,CLS_S3_Contig100,59,11,0.4055
CLS_S3_Contig100_st,CLS_S3_Contig100,61,11,0.4511
CLS_S3_Contig100_at,CLS_S3_Contig100,63,11,0.474
CLS_S3_Contig10031_st,CLS_S3_Contig10031,53,12,0.5548
CLS_S3_Contig10031_st,CLS_S3_Contig10031,57,10,0.4871
CLS_S3_Contig10031_st,CLS_S3_Contig10031,61,12,0.547
CLSS3627.b1_F19.ab1,CLS_S3_Contig10031,62,11,0.5129
CLSS3627.b1_F19.ab1,CLS_S3_Contig10031,64,11,0.5789
DATA

my %origins;
my $numColumns;

open my $inFile, '<', \$data;
while (<$inFile>) {
    chomp;
    next unless length;
    
    my @columns = split ',';
    
    $numColumns ||= @columns; # Assume first row has correct column co
+unt
    $origins{$columns[1]}[$columns[2] - 1] = \@columns;
}
close $inFile;

for my $oKey (sort keys %origins) {
    my $origin = $origins{$oKey};
    
    for my $pip (0 .. $#$origin) {
        my $row = $origin->[$pip];
        
        if (defined $row) {
            # pip exists in original file
            print join (",", @$row, '1'), "\n";
        } else {
            # pip doesn't exist in original file
            print ",$oKey,", $pip + 1, ',' x ($numColumns - 2), "0\n";
        }
    }
}
[download]

Prints (with large middle portion skipped):

,CLS_S3_Contig100,1,,,0
,CLS_S3_Contig100,2,,,0
,CLS_S3_Contig100,3,,,0
,CLS_S3_Contig100,4,,,0
,CLS_S3_Contig100,5,,,0
...
CLS_S3_Contig10031_st,CLS_S3_Contig10031,57,10,0.4871,1
,CLS_S3_Contig10031,58,,,0
,CLS_S3_Contig10031,59,,,0
,CLS_S3_Contig10031,60,,,0
CLS_S3_Contig10031_st,CLS_S3_Contig10031,61,12,0.547,1
CLSS3627.b1_F19.ab1,CLS_S3_Contig10031,62,11,0.5129,1
,CLS_S3_Contig10031,63,,,0
CLSS3627.b1_F19.ab1,CLS_S3_Contig10031,64,11,0.5789,1
[download]

which demonstrates what I understand you to want.

The key points are using a HoAoA where the hash is keyed by the origin and the array is indexed by PIP (- 1). Note that Perl generates the missing array elements, but sets them to undef so you can test for defined to see if you encountered the PIP in the original file.