Long-lived instances of internal classes (`ManagedType` and derived) should use `PyObject` instead of raw pointers

We have trouble keeping proper refcount balance on internal objects. For short-lived references, the problem is solved with `BorrowedReference` and `NewReference` types. For long-lived references we have `PyObject`, that ensures safety, however we are not using it in internal classes. There's very little reason not to do so.