I think what they are suggesting is that if a plugin that was already bundled with core was listed in app.yaml, then it would just be ignored. With a notification stating that including in app.yaml was redundant and the owner could remove it.
I too find it a little annoying that as long as I have any plugins listed in my app.yaml, I always run the risk of a failed update. So every time I do the update I need to double check to see if one of my plugins has been added to core.