Experiment: iPhone 7, iOS v 10.2.1, 2017 Ford Escape, Sync 3 v 2.0 with navigation
Plugged iPhone into USB, system prompted Apple CarPlay, I declined CarPlay, system indexed the iPhone, "USB iPhone" showed up in audio sources, I was able to browse, select and play music from the touch screen, I was able to use voice commands to select music, enabled CarPlay, checked function of CarPlay, disabled CarPlay, connected iPhone by USB, I was able to select and play music from iTunes by the touch screen, when I tried to use voice controls, the system responded "preparing device for voice commands" (not exact wording), tried again after a few minutes, same response, iTunes had 2 albums in it, iPhone did not have any apps to test out AppLink.
I will do more testing and let you know.