For posterity; the minimum you need to do is:

$PDL::BIGPDL=1; # true value
$name=zeroes($large_number1,$large_number2); # now size not checked
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An even better solution to the problem is to use PDL::IO::FastRaw and memory-map a disk-file, which doesn't allocate any RAM at all:

use PDL::IO::FastRaw;
$name=mapfraw(
  'fname',
  {Creat => 1, Dims => [$large_number1,$large_number2]}
);
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