I often had to poke around inside Atom to see what it was really doing, what some bug was, and to figure out how to write or configure extensions. I don't as often do that with Vim, but it's pretty clean C.

Do you not look inside the overly complex tools you use, especially beta ones? The whole appeal of "open source"/"free software" etc. is you can read the code. But if it's in something you can't stand, that's a disadvantage.