I have a fix for this up. Some refactoring will make this less awkward.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/add9e90c4c9f78106942717c988c41ee824d598d

commit add9e90c4c9f78106942717c988c41ee824d598d
Author: Christopher Cameron <ccameron@chromium.org>
Date: Thu Jan 17 06:13:58 2019

AppShim: Fix race when extension is unloaded

This bug has been present in ExtensionAppShimHandler for a very long
time, but has started appearing in the context of PWAs.

If an extension is uninstalled while it is in use, then there exists a
race in  ExtensionAppShimHandler::OnBrowserRemoved wherein may no
longer be an extension for the Browser, causing an early out, which
then causes two sources of badness (1) an invalid pointer hanging out
in |app_browser_windows_| and (2) the AppShimHost won't exit.

Fix the bug by doing a more thorough search through
|app_browser_windows_|, without reference to the actual Extension
pointer (as it may no longer exist).

Bug:  921456 
Change-Id: Ica1e2c40332e932f979791478d3dac1dab2c07a6
Reviewed-on: https://chromium-review.googlesource.com/c/1411214
Commit-Queue: ccameron <ccameron@chromium.org>
Reviewed-by: Dominick Ng <dominickn@chromium.org>
Cr-Commit-Position: refs/heads/master@{#623606}
[modify] https://crrev.com/add9e90c4c9f78106942717c988c41ee824d598d/chrome/browser/apps/app_shim/extension_app_shim_handler_mac.cc

Manually testing in Canary, looks like this is fixed.