Only create AppsNavigationThrottle for main frame navigation.

Currently we will create app navigation throttle for both main frame and
iframe navigations. This causes a issue where if there is a subframe
navigation it will overwrite the intent picker icon status that is
shown for the main frame. Previously a CL is landed
(https://chromium-review.googlesource.com/c/chromium/src/+/1609750) to
fix the issue by not showing the icon when there is a iframe. However if
a iframe navigation happens it will hide the icon even when the main
frame navigation request the icon to show. This CL fixs the issue and
adds tests for it.

BUG=964802

Bug: b/132641354
Change-Id: Ic7ce20daf4c7c7bd96eb48f112db2fd59214a14f
Reviewed-on: https://chromium-review.googlesource.com/c/chromium/src/+/1624073
Reviewed-by: Scott Violet <sky@chromium.org>
Reviewed-by: Dominick Ng <dominickn@chromium.org>
Commit-Queue: Maggie Cai <mxcai@chromium.org>
Cr-Commit-Position: refs/heads/master@{#662904}