I wonder if this is also the behavior for SW-initiated notifications.

+miguelg@ who is looking into moving to native notifications on OSX (though older versions will still have this issue even post migration)
+peter@ who knows web notifications best.

This seems to be specific to <cmd>+<h> - the bug does not show when the window is minimised, or other windows are on top.

Should something special be done when creating a notification toast in that situation to prevent the rest from Chrome popping up?

Yes, but I wasn't sure what the special thing was — turned out it was a one-line change, so I just made a CL :).
https://codereview.chromium.org/2399993003

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/a8cad7b0b4254bec43a95c58509f636236b262f2

commit a8cad7b0b4254bec43a95c58509f636236b262f2
Author: sdy <sdy@chromium.org>
Date: Fri Oct 07 14:39:29 2016

[Mac] Don't unhide Chrome when a notification is displayed.

Right now, if Chrome was hidden (cmd+h) and a notification comes in, the
whole app unhides.

Calling setHidden:YES on the notification window lets it be visible when
Chrome is hidden, and the -[NSWindow order*] methods respect it by not
unhiding the app.

BUG= 653266 

Review-Url: https://codereview.chromium.org/2399993003
Cr-Commit-Position: refs/heads/master@{#423856}

[modify] https://crrev.com/a8cad7b0b4254bec43a95c58509f636236b262f2/ui/message_center/cocoa/popup_controller.mm

 Issue 675733  has been merged into this issue.

Migrating to more generic platform label, so that it can be applied to other platforms (i.e. I love the idea).