His father started the Lindisfarne Association, which was a sort of highbrow hippie ecumenical colony, well known in the post-60s counterculture (somebody here will know a lot more about this than I do!), where the likes of Stewart Brand and the Dalai Lama would rub shoulders on panels. So he grew up around spiritual luminaries and consciousness-raisers. The American adaptation of Buddhism matured in circles like this, so he had a front-row seat, but from a child's perspective.
There's an interesting discussion at https://www.youtube.com/watch?v=heSq98tNTlM&t=9s between Thompson and Robert Wright, who wrote "Why Buddhism is True" and who, although he oddly insists he isn't, seems exactly the sort of well-intentioned Buddhist modernist the OP (and Thompson) are writing about.