You don't need to run perl through system, you can do that directly in perl:

#!/usr/bin/perl
use strict;
use warnings;

{   local ( $^I, @ARGV ) = ( '', 'test.txt' );
    while ( <> ) {
        s/#//;
        print;
        }
    }

{   local ( $^I, @ARGV ) = ( '', 'test.txt' );
    while ( <> ) {
        s/(?=.*\btest\b)/#/;
        print;
        }
    }
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