I've not had much issues understanding what runs when, because for the most part I didn't need to care that much, and when I did it was possible to order/schedule systems in Bevy. That's even a bit easier nowadays too, since the API improved!
With regards to the chaos: I think it can be avoided, but like you said it requires a bit of discipline. I don't feel like it required that much more than normal software engineering (but I'm also the type of person that documents and tests everything even on personal projects lol). The plug-in system makes it easy to help bring order too.
This is all through a bevy-tinted lens, since I've done very little game dev (dabbled with UE and Godot) outside of bevy, though!
With regards to the chaos: I think it can be avoided, but like you said it requires a bit of discipline. I don't feel like it required that much more than normal software engineering (but I'm also the type of person that documents and tests everything even on personal projects lol). The plug-in system makes it easy to help bring order too.
This is all through a bevy-tinted lens, since I've done very little game dev (dabbled with UE and Godot) outside of bevy, though!