The rules are not being applied out of a sense of ethical obligation, but rather to punish Boghossian for his views and for causing offense to other academics.

If he had done this outside of his university-affiliated research I bet the university would be investigating him anyway.

I bet the university and the academics he offended would also claim that nothing he publishes happens "outside" his university affiliation because everybody knows he is a professor there, he represents the university, he published articles in academic journals whose editors believed he was doing academic stuff, and so on.