The manga that says the dude is popular for no reason and then has the main character behave in largely the same manner and be popular in the same way?
In the original game Minato Shindou was not merely popular with the girls for 'no reason'. He is distinctly described as a "self centered" "ore-sama type", "a useless guy who relied on the girls for everything."
Merged with Mashiro Yukitsuki, Suzuna Amatsuki is very different in behavior. Even in the original scene, it was Suzuna who noticed that Riri was being harassed, and pointed it out to Minato. And now without Minato around, she still chose to stand up to the harasser despite being even smaller than Riri. Riri became interested in her for that savior moment, but she also seems to enjoy how skittish Suzuna acts, calling her "cute, like a cat on its guard".
With Kokona Shindou, it's harder to pinpoint the exact action that made her choose Suzuna. Suzuna helps Kokona with her cooking, but unlike in the original story she does it without a contest, while giving Kokona a convincing reason to stop treating her as an enemy. We know that Suzuna is just trying to manage things, but from Kokona's perspective Suzuna brought her a homemade bento as a peace offering, and then said something oddly inspiring. Suzuna was just improvising, but in those words Kokona recognized her own strange dynamic with her brother. It's also important that when Suzuna told Kokona that she appreciated the gesture but didn't want Kokona to cook for her every day, Kokona listened.
Granted, both Kokona and Riri are so extreme with expressing their interest in Suzuna that it comes across as contrived. She became relatively popular unreasonably quickly. But her sudden popularity is not contradicted by a repulsive personality. She has avoidant tendencies and a poor self-eseteem but she does not expect these girls to do anything for her. In fact, her main concern, other than her own fear of getting close to others, is to disrupt the lives of the original heroines as little as possible.