Unable to reproduce this issue on reported version 65.0.3325.146 and on latest stable 65.0.3325.162 using Ubuntu 17.10 with steps given in comment#0. Attaching screencast for reference.

1. Logged into facebook and got notification at top left end -- Hit ctrl+w -- (this closes facebook tab) -- Observed close of notification along with tab.
2. Got notification at top left end -- Hit ctrl+shift+q -- (this closes entire browser) -- Observed close of notification along with entire browser window.

@Reporter: Please check the video and let us know if we miss anything. Also please let us know on which flavour of linux you are seeing this issue. This would help in further debugging of issue.

Thanks!

Deleted: 821329.webm 4.7 MB

	821329.webm 4.7 MB View Download

Thanks but try this instead:

Wait six hours without any chromium running.

By this time we will surely have built up some Facebook notifications.

Now "accidentally" do
$ chromium

The single start page opens with some Facebook notifications overlayed
near the corner. (Lower right corner for me, lower left corner for you.)

Now within a second or two "realize" that we have no time to browse the
Internet, as the boss, or our bladder is calling, and we wish to close
the browser, which we do with a CTRL+W (as there is only one window.)

The browser closes, but we have to wait 15 seconds for the overlays to
disappear.

(Actually one might say they should not disappear, as the CTRL+W was not
directed at them, but instead the single window.)

In your movie you still have the chrome://version window open at all
times. I don't.

Thank you for providing more feedback. Adding the requester to the cc list.

For more details visit https://www.chromium.org/issue-tracking/autotriage - Your friendly Sheriffbot

(Note: the lower RIGHT corner notifications I am talking about have an X and cog-wheel in their upper right corners. If one clicks the cog-wheel one goes to
chrome://settings/content/notifications .)

As per Comment #3 we have waited six hours without any chromium running.Unable to reproduce this issue on reported version 65.0.3325.146 and on latest stable 65.0.3325.181 using Ubuntu 17.10 with steps given in comment#0
Steps
--------
1.Launched Chrome and navigated to www.facebook.com
2.Logged with credentials and closed window by using Ctrl+W 
3.As per comment #5 >Naviagated to ""chrome://settings/content/notifications"" observed notification are enabled.

@Reporter:Could you please let us know on which flavor of linux you are seeing this issue. This would help in further triaging of issue, also requesting someone from notifications team for help in further debugging of this

$ apt-cache policy chromium
chromium:
  Installed: 66.0.3359.139-1+b1
  Candidate: 66.0.3359.139-1+b1
  Version table:
 *** 66.0.3359.139-1+b1 500
        500 http://free.nchc.org.tw/debian unstable/main amd64 Packages
        100 /var/lib/dpkg/status

Thank you for providing more feedback. Adding the requester to the cc list.

For more details visit https://www.chromium.org/issue-tracking/autotriage - Your friendly Sheriffbot

Ctrl-W doesn't stop/close the *browser*, it closes the *window*.
Notifications are different windows that won't be closed with Ctrl-W.
This seems to be working as intended. At least it's consistent and makes sense.

To exit the browser immediately and completely use the dedicated shortcut Ctrl-Shift-Q or the Exit command in the browser menu.

OK I can confirm Ctrl-Shift-Q closed everything real fast.
So please close this bug.

As per comment#10 from the reporter closing the issue and marking it as Won't fix.

@Reporter: Feel free to raise a new one if you face the issue again.

Thanks!