All of the comments have either been: "that option doesn't do it", or "use a different module". Nobody managed to suggest either a fix/change for XML::Simple, or a set of options I can use that causes XML::Simple to become 'self-consistent' when dealing with partial content.

So in the end, I wrote a small post-processing routine to normalize the output from XMLin(). I.e recurse through the structure and a) promote leafs that are empty hashes to empty values.

 { } to  ''

and b) hashes that contain only the single 'content' entry into simply the value:

 { content => 'xxx' } to  'xxx'

Now I consistently get what I expected regardless of data content.

$VAR1 = \{
            'obj' => [
                     {
                       'class' => 'myclass',
                       'set' => {
                                'key2' => '',
                                'key1' => 'a'
                              }
                     },
                     {
                       'class' => 'myclass',
                       'set' => {
                                'key2' => 'b',
                                'key1' => 'a'
                              }
                     }
                   ],
            'name' => 'me'
          };
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Using the following:

sub reduce {
  my ($ref) = @_;

  if (ref($ref) eq 'REF') {       # recurse into references...
    $$ref = reduce($$ref);
  } elsif (UNIVERSAL::isa($ref, 'HASH')) {
    my @keys = keys %$ref;
    if (scalar (@keys) == 0) {    # empty hash becomes an empty string
      return '';
    } elsif (scalar (@keys) == 1 && $keys[0] eq 'content') {
      $ref = $ref->{$keys[0]};    # 'content'-only becomes the value
    } else {
      foreach (keys %$ref) {      # recurse into multi-element hashes
        $ref->{$_} = reduce($ref->{$_});
      }
    }
  } elsif (UNIVERSAL::isa($ref, 'ARRAY')) {
    foreach (@$ref) {             # recurse into arrays
      reduce($_);
    }
  }
  return $ref;
}
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