Hey, sorry for the late reply here - been working really hard the past few days incorporating feedback. Here's how the app looks like on the latest nightly build.
More improvements are on the way too

It's not your fault - the app should do better. Currently, if the changes 'touch', GB treats it as if they intersected... which can lead to this kind of confusion.

Soon the app will allow partial committing (vid below) & it will be possible to handle this better. Thanks for being patient with us! 🙇‍♂️

I'm so proud of the @gitbutler.com team <3! This is us, hacking on stacked branches, from just a few weeks ago

Same at our household 🙈