I agree that most manufacturers bundle nav systems with (sometimes unwanted) packages. For example, at least in the US, the Camry LE doesn't offer the option of a navigation system. You need to step up to the XLE which adds things like lower profile tires, leather and noise-reducing windshield. Subaru bundles the nav with a moonroof. With the Passat, you can get the nav option by itself for ~$700 on any trim level (except base maybe), which I think is reasonable.
I'm not sure what the justification is for these bundles (other than profits). However, automotive navigations systems probably have tougher standards to meet, they have to last the life of the vehicle. The portable ones can last a few years and no one would complain. Then, there are the additional costs of installing the gps antenna and wires (and possibly the reverse camera/wires).
It also seems to be becoming increasingly difficult to take apart dashboards to install aftermarket systems. You can't simply slide out the existing double-din unit and slide in a new one.
Phone nav systems seem excellent. However, most cars don't have a convenient/neat method to mount them. You end up having to glue/vacuum a platform to the dashboard/windshield and run an unsightly cable. I would love to have a dash slot where I could snap-in an LTE-enabled iPad Mini or some such tablet. Unfortunately, that is not going to happen.
Sony did introduce a dash unit that is compatible with phones and can charge without cables. However, the user interface apparently is half-baked and the dash unit itself doesn't look good.