Yeah.... I don't remember exactly how the yoyo badges work, but they are for the different projects within it, PrimeGrid is points for each project inside, I think.... It's been awhile since I really looked into it..... But since there aren't any bonus points, they could just as easily set a specific number of units for each badge....
But it does allow you to differentiate between the different projects inside them that you run, so it's not just about points.... Just like WCG, if one person only runs one WCG project and another runs all of them, the one project person would get a badge before the all project person even though they could very well have the same total points....
edit:
http://www.rechenkraft.net/wiki/index.php?title=Yoyo%40home/badges I can't find anything official for the PrimeGrid badges, but they are point-level based and change color....