The problem was that they used Ctrl + Alt for shortcuts, which is something you simply not do on Windows. Ctrl + Alt is the same as AltGr and there are keyboards without a right Alt key. AltGr + X looks like Ctrl + Alt + X, because that's what some people have to press. They are meant to be the same thing.

Chrome merely happened to implement that part of the UI Events spec (it's still a draft) which lets you differentiate between Ctrl + Alt and AltGr.

https://www.w3.org/TR/uievents/#code-examples

The Atom team simply could have changed their default shortcuts 2.5 years ago. Those shortcuts were the actual bug.