If you call down and up as functions rather than methods, you can avoid the need to share a reference.

use Thread::Semaphore qw( );
use threads::shared   qw( );

BEGIN {
   *sema_down = \&Thread::Semaphore::down; 
   *sema_up   = \&Thread::Semaphore::up; 
}

my $line_semi : shared = 0;

...
sema_down(\$line_semi, 1);
...
sema_up(\$line_semi, 1);
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Update: Alternatively:

use Thread::Semaphore qw( );
use threads::shared   qw( is_shared );

BEGIN {
   package Thread::Semaphore;

   no warnings 'redefine';
   sub new { 
      my $class = shift;
      if (@_ && is_shared($_[0])) {
         return bless \$_[0], $class;
      } else {
         my $val : shared = @_ ? shift : 1;
         return bless \$val, $class;
      }
   }
}

my $line_semi_count : shared = 0;
my $line_semi = Thread::Semaphore->new($line_semi_count);

...
$line_semi->down(1);
...
$line_semi->up(1);
[download]

Both methods are backwards compatible.