We use things like past perfect to make it clear what happened before something else. When you have a very clear marker like the word "before" the use of the past perfect isn't as important.
A is fine and traditional.
B. This is fine too because it's reported speech, which pushes thing back a step in the tense sequence, so the "arrived" can become "had arrived."
C is also fine. It's clear the train left, and then he arrived, in that order, both in the past.
What would not be okay is to say that the train left before he had arrived. Although it's still clear what is meant, you don't use the past perfect for the more recent action and the simple past for the earlier action.
There's no difference between "he said" and "he says" regarding the rest of the sentence. The only difference is that you probably have the person on the phone relaying what he is saying when you say "he says" (or you're translating for someone who doesn't understand). With "he said" it can be just as immediate, or it could have been six months ago.