Translator note: Aya now calls Mitsuki with her first name instead of "Koga-san". And Mitsuki makes a show of calling her "Oosawa-san" when speaking with Joe, but then, at the end, calls her "Aya-san".
The fact Mitsuki still uses a polite "-san" speaks volumes about who's on top.
For me this means that Mitsuki is on top but maybe I am misinterpreting your tone and you mean that Aya is on top?
It means that Mitsuki is more "respectful" toward Aya than Aya is toward Mitsuki.
Which implicitely means that Aya is "higher" in the hierarchy and "on top". Though I thought it was obvious all along the manga...
How you call someone carries very subtle implications in Japanese culture, because it's very hierarchical. Foreigners often trip on that and can inadvertently belittle someone without realizing it.
I am sorry I thought you were making a word play implying that Mitsuki was topping Aya, and Mitsuki still using -san was similar to the cookiness when a Kouhai tops her Senpai and is still very polite. Thanks for explaining! though I already know about that stuff, I thought what you said had a double meaning, I have my mind in the gutter lol