I don't think this involves deep questions such as conditional, counter-factual, etc. It's just that the pluperfect tense is fading away in modern usage. In both of your examples "If he had come" is correct in terms of sequence of tenses, but it sounds old-fashioned and people just don't bother to be correct anymore. Instead they tend to say "If he came" in both cases.
What I do not know is how long this trend has been going on. Probably all my life and I am 65. But maybe a lot longer. Scholars?