How is this an improvement? Is there a better way to Use IPC::Open3 instead of backticks?

It isn't, they're not equivalent, using open3 is like using open, not like using backticks,

as Perl::Critic::Policy::InputOutput::ProhibitBacktickOperators tells it, backticks is more like "capture" from IPC::System::Simple

Capture::Tiny is what you want

use Capture::Tiny qw/ capture /;
my @cmd = ( "...ls", 'dir' );
my( $stdout, $stderr, $exit ) = capture {
     system { $cmd[0] } @cmd;
};;
$exit and die "it failed with $exit and $stderr ";
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Also of interest might be String::ShellQuote/Win32::ShellQuote