$ perl -Mstrict -Mwarnings -E '
    no warnings q{qw};
    my @file_data = (
        [qw{target1,48,12,7 target2,17,16,2 target3,22,6,1}],
        [qw{target5,14,12,8,,3, target6,5,7,9,,,15}],
        [qw{target1,,,,,,13 target2,,,,,,8 target4,,,,11,5,6}],
        [qw{target1,,,,51,8 target2,,,,87,42 target4,22,3,7,,}],
    );
    use warnings q{qw};

    my %merged;

    for my $file (@file_data) {
        for my $line (@$file) {
            my ($row_val, @values) = split /,/ => $line;
            
            for (0 .. $#values) {
                if (! defined $merged{$row_val}[$_] 
                    or ( ! length $merged{$row_val}[$_] and length $values[$_] )
                ) {
                    $merged{$row_val}[$_] = $values[$_];
                }
            }
        }
    }

    say join q{,} => $_, @{$merged{$_}} for sort keys %merged;
'
target1,48,12,7,51,8,13
target2,17,16,2,87,42,8
target3,22,6,1
target4,22,3,7,11,5,6
target5,14,12,8,,3
target6,5,7,9,,,15