Next Gen Team Seven really is a bunch of misfits… almost more than canon original Team Seven given that instead of the Boruto=Naruto, Sarada=Sakura, and Mitsuki=Sasuke setup that Kishimoto was no doubt going for, it becomes Sakako=Sasuke and Mitsuki=Sakura and that’s HILARIOUS. Not in their preteen crush kind of way, but just as their personalities/origins/dynamics.
Boruto and Sakako do not get along at all. Mitsuki is a weird fanboy of all of the original DoS Team Seven so he’s not biased towards one or the other buuuuuut he’s not exactly the bridge between the two of them.
Ah, yeah, she and Boruto eventually bond–no doubt during a mission gone wrong as you said. Probably her ability to see ghosts is part of the reason why they bond: that’s how they escape the situation that separated them from Mitsuki and Konohamaru-sensei. His ghosts guide them out maybe? And he promises to keep her secret.