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Rather than closing popups immediately, we should close the popups with
animation and let MessagePopupCollection::Update() close them
eventually.

Ideally MarkAllPopupsShown is problematic and this should be cleaned up
along with UiController, but for now the fix should be acceptable as it
just replicates the behavior of old MessagePopupCollection.

Steps to repro:
1. Create a notification
2. Click on a notification

TEST=manual(asan build)
BUG=869593,869716

Change-Id: Ifdfc7c2a362727740401e6e16845d8d770877730
Reviewed-on: https://chromium-review.googlesource.com/1158118Reviewed-by: Yoshiki Iguchi <yoshiki@chromium.org>
Commit-Queue: Tetsui Ohkubo <tetsui@chromium.org>
Cr-Commit-Position: refs/heads/master@{#580087}