It gets really technical with the math, analyzing std. deviations away from spell averages, etc. I add in my own opinionated weights too. It's my colonels secret recipe, haha.
Yeah, there will always be oddities. Popularity is an authoritative list of what spells people add (on 5e Spellbook Builder), Appeal will always be an interpretation of that data. I think it's more truthy and useful than misleading or I wouldn't have released it. It's most useful when you use the filters, and look at specific classes or levels. Seeing how much appeal Eldritch Blast has over Hunter's Mark is obviously not meaningful.