Change 306560 had a related patch set uploaded (by Mooeypoo):
Append mw.notify div to the body so it appears on top of everything

https://gerrit.wikimedia.org/r/306560

Posting my answer to the discussion in the commit:

Regarding the first point - in vector, it works as intended, but in monobook, the overlay is on top of the personal toolbar now. I can change this with a style change to monobook (and it shouldn't be a bad idea to let skins decide where to pop that notice out, I think) - but that does raise the question of whether this is something that should be forced onto the skins to deal with or not, and it definitely make point #2 more important.
The main issue that raised the need for this here is MobileFrontend's usage of mw.notify. We wanted to add an mw.notify popup confirming that "x notifications were marked as read" when a user clicks the "mark all read" button in the overlay. This doesn't work if the mw.notify div is inside the content but the MobileFrontend overlay is outside it.
So the question now is what is more proper and what is better -- changing mw.notify to always be on top (in my opinion seems like a good behavior for global notification popup) or leave mw.notify as-is and claim this is a specific issue with MobileFrontend's use of it (or assume any other extension/tool should solve for this individualy)

@Esanders pointed out an idea that would fix both issues:

mw.notify can create two sections to overlay the popup - the default would be in the content (like it is now) but another would be "global" overlay in the body as a redundancy. When we call mw.notify() we can explicitly state to use the global one when needed.

That would solve all issues, it seems, and be "backwards compatible" for skins and whatever extensions or gadgets that use the current behavior.

You should give the global overlay an additional class so it can be positioned differently if required.

So this sounds like a good idea, and it should work - but the way that mw.notify is written right now, there are a lot of assumptions that all notifications are in the same known $area block. Setting up two area blocks, one in content and one global would require a significant change to the way things work.

I can definitely tackle this, but this will no longer be a trivial small change to the code.

Change 306560 had a related patch set uploaded (by Mooeypoo):
Add an option for global overlay in mw.notify div

https://gerrit.wikimedia.org/r/306560

Change 306560 merged by jenkins-bot:
[mediawiki/core@master] Allow skins to place notification container for mw.notify

https://gerrit.wikimedia.org/r/306560