Erm, that's not what I meant and I suspect you know that. I didn't assert it was "a magical [something]" or anything, just bad UI. Open Notes, edit a document, close it, go away, expect it to be synced on your iPad: fail. And no normal user will do CMD-S, that was the whole point of them abolishing explicit document saving.
Notes are synced without you needing to do anything. If you close the application before a sync is polled (within 5sec after you stop editing as far as I can tell) why would you expect it to sync? That's like sending an email and closing the browser while it's posting the data and then being mad it didn't send.
"Sending an email" is something the user initiates. "Syncing to iCloud" is something the OS initiates.
Also, I would hope that "sending an email and closing the browser window", one day, will work like "sending an email and quitting the mail app" works today.
Power Nap is meant to do this - keep stuff syncing, backing up, etc regardless of lid state. Now, whether it's smart enough to flush any synchronizations that are still in progress when the lid is closed or you have to wait a few minutes until it half-wakes-up and does its thing, I'm not sure. Also, I believe by default it's off when a power supply isn't attached.
Right clicking on the document title will give you the nested hierarchy of where it's saved. If its saved to iCloud right clicking shows 'iCloud'.
Unsaved program files are saved in ~/Library/Caches/com.apple.iWork.program; it isn't a particularly magical or a trap.