But there's no way I know to exclude the 32-bit perls

You would just want your CPU-x86_64-InstructionWriter-0.002 Makefile.PL to begin with:

use strict;
use warnings;

use 5.010000;

use ExtUtils::MakeMaker;

if($Config::Config{ivsize} != 8) {
  warn "This module requires 64-bit integers";
  exit 0;
}

# existing code then follows, unaltered.
[download]

I don't know how you achieve that alteration using Dist::Zilla to generate your Makefile.PL, but cpantesters would then report your module as "NA" instead of "FAIL".
Anyway, adding support for 32-bit integers might be a more interesting exercise ;-)

Cheers,
Rob