Having standalone libs doesn't automatically make it update without externals. Choosing "Update all Installed Addons" (F12, I believe) will do it without externals. You could still tell WAU to update with externals, but.... then you'd have libs in all your addon folders again.
It's up to you, bertlezat, whether you want to keep the preferences changed or not. I switched mine back to defaults. If you leave skip version check set to True, it will update all of your addons all the time, whether they have a new version or not. If you leave delete before extracting set to true, it will always delete the old addon before installing the updated version. Some people like to do this, just to make sure they always have clean installs (helps if an addon goes through a major revision and deletes some files/folders), but if you add things to an addon (like a layout to ag_UF, for example) you'd have to go back in and add it again. It's always a good idea to back up your Interface folder before running the WAU so you can revert to previous versions if needed or have a backup to copy-paste custom changes you've made to an addon.
Remember, anyone reading this, that Ace2 was built so that you could use embedded libraries. I repeat again to not bother with standalone libraries unless you really want a smaller file size for your Interface folder, have problems with your libraries often, or feel that it will have you troubleshoot/bugfix things. Having 30 copies of Ace2 in each addon folder will not impact your game's memory usage, since the game only loads one copy of each library.