This fixes
UrlOverridingTest#testNavigationFromXHRCallbackAndLongTimeout
ToolbarTest#testNTPNavigatesToErrorPageOnDisconnectedNetwork
externalnav.UrlOverridingTest#testNavigationFromTimer

Once is_external_protocol was set correctly, the second bug that happened was because with PlzNavigate we were making requests for chrome-native schemes. This caused NavigationHandleImpl::WillStartRequest to be called, which added navigation throttles and that ended up calling the Android navigation interceptor. It's not called without PlzNavigate, which led to these tests failures.

BUG=659089

Review-Url: https://codereview.chromium.org/2760463005
Cr-Commit-Position: refs/heads/master@{#459285}