My understanding has always been that, while some Buddhists do in fact proclaim belief in various deities (Tibetan Buddhism in particular), there is always an acknowledgement that they only exist in the realm of the mind. That is, subjective experience is elevated and the idea that "objective reality" can be experienced is discarded. The common word for this is Nondualism. And this Tim Maudlin person does confess to being a non-dualist.

I agree that the tone of the Scientific American article was annoying and somewhat condescending. But overall I don't have any issue with the ideas presented. I don't see the conflict.