pybind: Should fix "RuntimeError: Instance is registered" when handling unique_ptr release workflows

[EricCousineau-TRI]

See pybind11 fork PR:

• class_: Register reclaim_from_cpp with constructing type pybind11#33

Related places where we got bit in Drake:

• py systems: Bind System.SetDefaultContext and Simulator.reset_context #12368
• integrators: add python bindings for dense integration #13044 (review) - commit and line

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Basically, I think this happens when you get a non-owning reference to something in C++, but then try to own it afterwards.
e.g.

class Stuff {
 public:
  T* get_thing();
  unique_ptr<T> release_thing();
};

obj = Stuff()
thing = obj.get_thing()
obj.release_thing()

[EricCousineau-TRI]

I believe I've gotten the fix working now (I had it way back in November, just wrote a bad test where I forgot to use rvp::reference_internal).