As long as you are not using threads, I see nothing non-optimal in your solution.

My sleepy mind just inverted the solution; use a wrapper that just does chdir and exec the command.
Untested code:

my $new_dir = "/usr/bin";
my $wrapper = 'perl -we chdir(shift)and(exec@ARGV)';
my($wtr, $rdr, $err);
my $pid = open3(
  $wtr, $rdr, $err,
  "$wrapper $new_dir some cmd and args",
);
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Kludgey. I like your current method better.