The consensus seems to be that the flange is a residuum (OK, a leftover?) of construction, and could theoretically be ground away without ill effect. That's extra work, but could be invoked if a new rub rail didn't fit snug, or if the flange was irregular. Just grind it down a little here and there.
The aluminum rub rail replacement alternative, although expensive, does fit over the existing flange without issue. That's what I have used, and the write-up is here .