In spite of what Johnson & others say, the real issue is not
scientific methodology. That is like southerners in the 1850s saying
that the issues were states rights, tariffs, &c. when the issue was, in
fact, slavery. The real issue here is evolution and, in particular, the
Darwinian component of it. The reason Johnson is popular among many
Christians is not because people are excited about epistemology but
because they want to have an excuse to relegate evolution to a minor
role (or deny it entirely) & not have to think about it or wrestle with
the religious issues it raises.
This is not to say that the question of "methodological
naturalism" is unimportant for scientists & those involved in scientific
dialogue. I think it is important, & that Johnson is profoundly wrong
about it. But that is not why his influence is so baneful.