[Shortcut] Do not auto update for shortcut with no manifest.

When we turn on the flag to CreateShortcutIgnoresManifest, we should
stop auto update the shortcut, otherwise it will get the manifest
and upgrade itself to a web app if the start url is the same.

This is essential for Chrome OS because we are introducing different
UI for shortcuts. However, it also seems to make sense to stop
the update for other platforms becuase if we want to be able to
create shortcut ignores manifest, we should not update the app to
use the manifest soon after. However I'm happy to only change this
for Chrome OS if we decide to not update this for WML.

BUG=1412708

Change-Id: I0d2468ceccb6dc63fd538b07b58df0d8e1f0fc45
Reviewed-on: https://chromium-review.googlesource.com/c/chromium/src/+/4899979
Commit-Queue: Maggie Cai <mxcai@chromium.org>
Reviewed-by: Glen Robertson <glenrob@chromium.org>
Reviewed-by: Daniel Murphy <dmurph@chromium.org>
Cr-Commit-Position: refs/heads/main@{#1203032}