So what you're really doing is comparing one rare pair (e.g. Neville/Charlie) to all other rare pairs in the category (e.g. slash-not!Draco/Harry, Severus/Harry, Ron/Harry, etc.) if I understand you correctly. I'm not sure sure that's fair to the straddling-the-fence pairings.
Let's say hypothetically that Harry/Luna is 3% of all het fics. That makes it rare. But if you excise all popular pairings, then it would probably be 10-15% of what's left. That makes it not rare. So, which is it? I would still call it a rarepair, because its presence in fandom is substantially lower than other pairings as a whole.
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Let's say hypothetically that Harry/Luna is 3% of all het fics. That makes it rare. But if you excise all popular pairings, then it would probably be 10-15% of what's left. That makes it not rare. So, which is it? I would still call it a rarepair, because its presence in fandom is substantially lower than other pairings as a whole.