Hi Gordon,
So, in order to correct my confusion perhaps you'd unpack your 'naturalism is an ontology' statement, just so that I understand your thoughts.
Relax, you're fine - science takes naturalism (in the sense that the natural is all there is) as a working assumption because natural phenomena are all that the tools of science can access and investigate. The switcherooo he's attempting is to conflate the working assumption version with an absolutist epistemic version - ie, the natural is necessarily all there is - so as to create a straw man he can dismiss.
I suppose that if you looked hard enough you might eventually find someone who does argue for the absolutist version, but they're few and far between I'd have thought for the fairly obvious reason that you cannot eliminate the possibility of unknown unknowns, however unlikely.
Of course none of this has anything whatever to say to whether there actually
is a supernatural, let alone to how it might be populated - ie, with gods, leprechauns or the man on the moon for that matter - so all he has is an "anything might be", with which no-one disagrees in any case.