Using pack will speed this up enormously. Besides that he wanted the numbers before the strings, so default to 999 instead of 0):

$ref = [
    map  { $_->[0] }
    sort { $a->[1] cmp $b->[1] }
    map  { my $srn = lc $_->seq_region_name;
          [ $_, pack "sA*", $srn =~ /^[0-9]+$/ ? $srn : 999, $srn ]
          }
    @$ref ];
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