[SottoVoce]

Actually the WAU updates the libraries the way you configure it to.

If you tell WAU to install the !!!StandaloneLibraries it will do just that and then delete the embedded libraries from all the Ace2 Add-Ons to decrease initial memory use.
After you've done that WAU will always update the addons without externals (meaning no embedded libraries).

By the way, after going through the list of installed add ons in the WAU unselecting all Ace Add ons mentioned in the Mazzle FAQ as modified/critical-to-be-updated I thought "What the hell" and just updated ALL installed Ace Add Ons.
What do you know? It works perfectly fine, nothings broken, everythings updated.

Only error BugSack throws is something from Quixote which, I believe, isn't even originally installed with MazzleUI, I think it came along, when I installed FuQuestFu (which I really like, btw, disabled Monkey Quest after trying QuestFu for a few days).