In my opinion, the NEC in 250.4(A)(1) is talking about limiting the voltages on the electrical system that result from outside influences such as lightning. Note that it does use the word system in this section. The other parts of this section use the word "equipment" and for the most part also uses the words "fault clearing path". I don't see anything that requires lightning protection of the electrical equipment or other conductive equipment in the NEC.
Don
