You're right, I didn't specify a value for the hash, because it doesn't contain anything -- it's XS code acting like a hash, or in the problematic case, XS code acting like a scalar.

I tried the following which appeared to work in a trivial test case, but it corrupted memory causing a Segfault in another location when I tested it in real code:

my $aref = $f->getVariants(); # reference to array containing many Foo
my $sfoo = shift(@$aref);

my $tiefoo = {};

# warning - this causes segfaults
bless $tiefoo, 'Bar::Foo';
tie %{$tiefoo}, 'Bar::Foo', $sfoo;
$tiefoo->ACQUIRE();
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So my conclusion is that it's not possible to fix this in pure Perl. The C++ or SWIG wrapper code must be modified.

because it doesn't contain anything

Creating an empty hash is very easy...

There's obviously some information the module requires from this hash. You can't create a hash that meets the module's needs until you figure out what this information is. This is what you need to do first.