I can replicate this on Linux (69.0.3493.3) and Windows (70.0.3503.0) as well but not on Mac (70.0.3502.0). I also checked that it still repros on ChromeOS 70.0.3502.0.

I'm curious what change broke this, especially since it is working on some Views platforms but not others. Other UI that breaks keyboard close shortcut (from a very quick test, so likely very non-inclusive):

* Bookmark bubble
* Page Info bubble
* History bubble
* Chrome menu
* Context menu in omnibox
* Extension context menu

Notably, the Cookies popup and Connection Info popup do not prevent the keyboard shortcut from closing the tab.

Also notable is that the permission popup visually takes the focus off of the main Chrome window when it pops up. Clicking outside the permission prompt (such as in the content area of the page) refocuses the main Chrome window without dismissing the prompt. After doing that, the keyboard shortcut works again.

To reproduce on Linux/ChromeOS/Windows:

1. Open https://permission.site
2. Click "Notifications"
3. With the permission prompt open, try to close the tab using Ctrl+W
4. The tab does not close

Hm. That means it's not the permission prompt itself. +robliao for Views, +erikchen who worked magic for hotkeys on MacViews (and so possibly knows why it works on Mac, but not elsewhere.)

There is likely an incorrect implementation of HandleKeyboardEvent somewhere.

See: https://chromium-review.googlesource.com/c/chromium/src/+/1097206

and possibly: https://chromium-review.googlesource.com/c/chromium/src/+/1067860

Some potentially related bugs I just stumbled across: Issue 319109 and  Issue 807643 

Able to reproduce the issue on Win-10 and ubuntu 17.10 using chrome reported version #67.0.3396.99 and latest canary #70.0.3506.0. Issue is not seen in OS-mac.
This is a non-regression issue as it is observed from M60 old builds. 

Hence, marking it as untriaged to get more inputs from dev team.

Thanks...!!