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OK, something appears to have gotten confused along the way here. Barry's original problem report was that operator.index() was returning a different answer than operator.__index__() for int subclasses. Absolutely nothing to do with the int builtin at all. While the fact int() *may* return int subclasses isn't especially good, it's also a longstanding behaviour.
The problem Barry reports, where a subclassing based proxy type isn't reverting to a normal integer when accessed via operator.index() despite defining __index__() to do exactly that should be possible to fix just by applying the stricter check specifically in PyNumber_Index.
Expanding the scope to cover __int__() and __trunc__() as well would be much, much hairier, as those are much older interfaces, and used in a wider variety of situations. We specifically invented __index__() to stay away from that mess while making it possible to explicitly indicate that a type supports a lossless conversion to int rather than a potentially lossy one.