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In 1.1 we long ago decided to accommodate NaN != NaN by allowing equality to not be reflexive (not require x = x for all x). In doing so, we failed to delete this parenthetical statement in 2.2.2 (and must do so if they choose to consider them identical) which would require that other applications treat NaN as equal to itself even though we don't.
On 19 December the XML Schema WG accepted a wording proposal to delete the parenthetical in question. Accordingly, I'm marking this closed.