Note: It doesn't matter which routine you call only that the filehandle as a scalar in the argument list. So it seems to be an artifact of Perl trying to munge the argument list into a C structure.

#!/usr/bin/perl
use strict;
use warnings;
require 'sys/syscall.ph';

my $buffer = "                ";

open my $f, '</dev/null' or die "open: $!";

# This works
syscall(&SYS_read, fileno($f), $buffer, 1) != -1 or warn "write: $!";
defined read($f,  $buffer, 1) or die "First pass, read: $!";

# This closes $f
syscall(&SYS_read, fileno($f), $buffer, 1, $f) != -1 or warn "write: $
+!";
defined read($f,  $buffer, 1) or die "Second pass, read: $!";
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Since there would be no C function that took a Perl filehandle as an argument, the appearance of a Perl filehandle in a syscall argument list I take to be an error.