I think there's also some influence from the pre-game groupings.
See, back when they were under the Perfect Dream Project codename, the original nine were put in groups of three for a set of 4koma running in different venues. The Famitsu app got Rina, Ai, and Ayumu, and is the memetastic one where Ayumu's a jerkass until Nozomi exorcises her, and then they all go to Mars; the SIF app itself got the three girls who'd previously been N idols in SIF, Shizuku, Kanata, and Emma. So Dengeki Online got the 4koma with Setsuna, Karin, and Kasumi, and for some reason a lot of early shipping featured those three in different combinations. (I think ShizuKana got some of that early boost well, and of course RinaAi went on to be reinforced by the game.)