flock implements advisory locking, which means that other applications are free to ignore the lock. The Windows emulation of flock uses mandatory locking, which means that other applications cannot ignore the lock.

Here's one way of doing the same without the extra file:

use strict;
use Fcntl qw( LOCK_EX SEEK_SET );

my $file = 'data.file';

open(my $FH, '>>', $file)
   or die("Can't open $file: $!\n");
flock($FH, LOCK_EX);
seek($FH, SEEK_SET, 0);
truncate($FH, 0);
...
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