Unfortunately I don't have a Windows machine handy at the moment, so I can't answer your question directly. The IPC::Run3 docs do say this:

For each redirector $stdin, $stdout, and $stderr, run3() furnishes a filehandle: if the redirector already specifies a filehandle it just uses that

Running the following test on Linux with strace appears to show this is true even for Perl's in-memory filehandles:

use warnings;
use strict;
use IPC::Run3 'run3';

my $in = "Foo\nBar\n";
my $out = "";
# This uses temp files:
#run3 ['/bin/cat'], \$in, \$out or die "run3";

open my $infh, '<', \$in or die $!;
open my $outfh, '>', \$out or die $!;
run3 ['/bin/cat'], $infh, $outfh or die "run3";
$?==0 or die "$?";
[download]

If that doesn't work, you might also want to give IPC::Run a try.

AFAIK many IPC modules have similar issues on Windows, I think that's part of the reason why IPC::Run3 uses temporary files often - it's more reliable (just compare the CPAN Testers Matrix of IPC::Run3 with any other IPC module).

BTW, you're worried about efficiency, but haven't said what kind of a load you're expecting - are you sure this isn't premature optimization?