Redunant Notification: "different layers than the imported version... to change this behavior go to"

Yep, it would be nice to have a way to hide that notification. Maybe right under "Hide new layers when updating or relinking" in the Preferences? If you wanted to make a feature request, you could head over to indesign.uservoice.com, where you'd have to make a new account to make a feature request. I'd upvote it!

Reason being is that I once had a project like yours, with a few hundred (386) of those windows to click through. But I was doing the update of the placed InDesign files in fifteen languages, which is close to six thousand clicks for a single update.  I knew I'd be updating once a week, as well. So I wrote a tool in AutoHotkey that would click the correct number of times, and set it up so that I could update all the links, run the .ahk script, and walk away from my computer for long enough to get some more coffee. Drank a great deal of coffee during that project! Something like that may be of use in your case, although it may take you just as long to learn how to write that script in AutoHotkey as it would to click through 186 of these dialogs.