Whitespace to make things easier to read is *completely* within the eyes of the beholder. Most often, I find *removing* extraneous redundant annoying empty lines improving the readability and maintainability. Also cleaning up is only useful if it matches the style of the surrounding project/script/module(s) after the cleanup. e.g. your cleaned-up code would not fit my standards and my code would not fit yours..

And if you clean up, why not go further?

foreach my $key (grep { !m/\t0$/ } keys %data) {
    my ($chr, $fivep, $threep, $strand) = split m/\t/ => $key;
    say join "\t" => $chr, $fivep, $threep, "-",
        map { $data{$key}{$_} // 0 } @files;
    }
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Less lines more to the point, no need for empty space as each line is clear on itself.

Personally, I'd use Text::CSV_XS with sep => "\t" like this:

use Text::CSV_XS qw( csv );

my @key   = qw( chr fivep threep strand );
my @files = qw( file1.tab file2.tab );

my %c7;
foreach my $file (@files) {
    csv (in     => $file,
         out    => undef,
         sep    => "\t",
         strict => 1,
         on_in  => sub { $c7{join ":" => @{$_[1]}[0..3]}{$file} = $_[1
+][6] }
         );
    }

say join "\t" => @key, @files;
foreach my $key (sort keys %c7) {
    say join "\t" => (split m/:/ => $key), map { $c7{$key}{$_} // 0 } 
+@files;
    }
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