I think Mochizuki has ulterior motives, but maybe I'm being paranoid.
We've been down this road before, she's intense in the way she displays affection but from what we've seen of her actions (after numerous encounters) she's genuine.
Think about it from this perspective, the way Tanuki goes about "making his sister understand" is his oppressive way of showing love for her. Mochizuki then acts as a foil to Tanuki but essentially being the same thing to HIM which should lead to him getting a different perspective on how he's going about behaving around his sister. She serves as a mirror for Tanuki to hopefully come to terms with his honestly kind of creepy attachment and methodology.
Even the things she does behind the scenes are very similar to what Tanuki has done. I guarantee Tanuki would have judo thrown the creepy perv teacher just like she did if he knew what he was planning. She manipulates Tanuki's activities and plans in the same way Tanuki manipulated his sisters. There is a poetic irony that Tanuki finds her annoying and considers her a "yandere" when she's very much just a female version of him.
I couldn't tell you where the author wants to take her character other than acting as a reflection of Tanuki, but as far as her having "ulterior motives" or being otherwise antagonistic towards him I wouldn't worry too much anymore than I would worry about Tanuki doing the same to Komaru.