I like the new arrangement with read-only Default Settings. (The menu item should probably say “read only”, since in Sublime Text 2 there were some settings which only worked in the Default Settings, and so required changing it.)
I copied the Default Settings into the User Settings, but when I installed BracketHighlighter, and some other package before that, it over-wrote the User Settings and removed all the helpful comments.
I did not use the menu to update User Settings. I just installed a package.
Fortunately I still had the User Settings open, so I was able to ctrl-x back to the earlier version.
I would like to be able to install packages without removing all the comments from the user settings.
Isn’t this the symptom of an unwanted side-effect?