What is mystical experience and what role should it play in religion? Is it a confirmation of the existence of God? If a convinced naturalist has mystical experience does that negate the confirmation aspect for the believer or is it evidence of the limitations of the naturalist's schema? I think the latter because the evidence for the natural roots of the mystical experience is overwhelming. Usually this experience is subsumed under the religious tradition that the mystic belongs to and indeed it often takes the standard forms that are validated by that tradition.
So how does the naturalist mystic fall short of a full understanding? For a start the interpretation of all events as having their roots in causal mechanisms that are material in origin is inadequate. Secondly the incoherence from their own point of view of the judgement of 'sameness'. One doesn't have to be a rabid Wittgensteinian to doubt this equivalence. It is just not demonstrable and therefore ought not to be considered by a thoroughgoing naturalist.
Then there is the variety of forms that mystical experience takes even within a single tradition. Why does the Blessed Virgin not appear to Hindus, does she not like them? Is she sniffy about Protestants too? Here the concept of ishta devata comes in: God will appear to you in your chosen form to strengthen your faith. What it may be asked is the faith that naturalists have that needs to be strengthened? They have a self, a nature, a consciousness which links them to the divine. That's quite enough to be going on with.