Luke says that even naturalistic philosophers exhibit these bad habits. He does not say that naturalism is a bad habit, or that it's a bad habit because it uses science to understand the world.

Not quite:

reading too much mainstream philosophy ... is somewhat likely to "teach very bad habits of thought that will lead people to be unable to do real work."

"Teach" implies that engaging one's self with "too much" mainstream philosophy will cause bad habits to arise (and make one unable to do 'real work', whatever that might be).

Unexamined presuppositions make a wonderful basis for discourse.