I'm not sure that Filter::Simple is supposed to work with both, the filtering code and the filtered code in one file. I've split up your code into two files and then changed executable_no_comments to code and now it works :)

#!/usr/bin/perl
package LanX;
use strict;
use Filter::Simple;

my $transform = sub {
        warn "$_";
    s{ X(\w+)\[ }
     {\$$1->\[}xg;
    s{ X(\w+) }
     {\$$1}xg;
    warn "=> $_";
    $_;
};

FILTER_ONLY "code" => $transform;
#FILTER_ONLY "executable_no_comments" => $transform;

1;
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and

#!/usr/bin/perl
#use strict;
BEGIN {
    require '732082-f.pm';
    LanX->import();
};

Xarr=[1..3];
print "@Xarr";
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