"If he come" vs. "If he comes"

Consistent with its non-factual status, the if... verb may be in the plain form, marking the subjunctive construction. Subjunctive in conditionals is rare, especially with verb-forms other than be. It belongs to the formal style and verges on archaic. (CaGEL p1000)

In the first sentence if he comes is an open conditional: his coming is not viewed as unlikely. In the second if he come also falls into the category of open conditionals, and similarly the speaker would not think his coming unlikely (CaGEL p745).

So, it seems there is little difference in meaning, but a clear difference in style: the first being idiomatic present-day English, and the second being formal or even archaic.

To my ears, the second sounds absolutely unacceptable in any context whatsoever.