many prefs changed after "cloning back" a Sandbox to the underlying drive

[camner]

Interesting....so here was my workflow:

1. (I'm booted off of the Sandbox) Copy back Sandbox to Underlying Drive using Smart Backup
2. Boot off of Underlying Drive to make sure things work well. Normal startup, including all of the login items (Yup! It's all good)
3. Boot off of Sandbox. Whoops! Lots of new pref files, including com.apple.loginitems.plist and loginwindow.plist and none of the previous login items load.

Now, I want to very what I think is correct, which is that the Sandbox and the Underlying Drive share the entire User folder via symlinks, so that the the Sandbox version of the user prefs folder is pointing to the Underlying Drive version of the user prefs folder. In other words, one is not a copy of the other but they are the same folder being pointed to via symlinks, right?

I think my next step will be to see if this sequence of steps leading to this end result is reproducible or just one of those odd coincidences.

Thanks for your quick reply, as always.