I did use the create-project.py to make my project.
Flickering only happens on Android, web & iOS is perfect.
Its not really an issue for me now, because i pass in the z-index value, but someone else might run into it, and not know whats going on.
If you want to replicate, add a background sprite to the demo above.
add this at the beginning of the code:
var background = cc.Sprite.create(background);